Autophagy maintains intestinal stem cell integrity

The intestinal epithelium is continuously renewed by a pool of intestinal stem cells expressing Lgr5. We show that deletion of the key autophagy gene Atg7 affects the survival of Lgr5+ intestinal stem cells. Mechanistically, this involves defective DNA repair, oxidative stress, and altered interactions with the microbiota. This study highlights the importance of autophagy in maintaining the integrity of intestinal stem cells. Intestinal stem cells and their direct transit amplifying progenitors from individual Lgr5-EGFP-IRES-CreERT2 (WT) or Atg7(fl/fl);Lgr5-EGFP-IRES-CreERT2 (Atg7KO) mice treated with tamoxifen were enriched by sorting CD24(low)/EGFP(High) or CD24(low)/EGFP(Low) populations, respectively. RNA was extracted using the RNeasy Micro Kit (Qiagen), reverse transcribed with the Ovation Pico System V2 (Nugen), then the resulting cDNA was fragmented and labeled with biotin using the Encore Biotin Module kit (Nugen). cDNA from 3-4 EGFP(high) and EGFP(low) samples was hybridized to GeneChip® Mouse Gene 2.0 ST (Affymetrix), scanned with a GCS3000 7G, and analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files).