We have dissected impact of a western style purified diet (NWD1) on intestinal and colonic tumorigenesis. NWD1 recapitulates mouse intake of key nutrients each at their levels epidemiologically linked to higher risk for intestinal cancer in western developed countries. We established that NWD1 amplifies and accelerates intestinal tumors in many mouse genetic models, regardless of genetic etiology and aggressiveness driven by single or multiple genetic drivers. Moreover, when fed to wild-type mice long-term, we and others established that NWD1 causes sporadic intestinal and colon tumors. At least 1 year before these sporadic tumors develop, there is altered maturation of epithelial cells and underlying molecular pathways in the histopathologically normal mucosa. This led to investigating how the cell and molecular biology of intestinal stem cells are altered by the NWD1, We reported the surprising discovery that NWD1 compromises stem cell functions of Lgr5hi cells in intestinal homeostasis and tumorigenesis, but that this is compensated for by mobilization of Bmi1+ cells as stem cells for these functions. Moreover, genetic and dietary experiments identify decreased vitamin D exposure and Vdr signaling as important in these effects, consistent with Clevers' reported stem cell expression signature strongly implicating Vdr signaling in Lgr5hi stem cell functions. Further, we noted that mouse experiments on intestinal stem cells have used diets establishing vitamin D levels well above the range of that for the US population. This raises significant questions regarding which and how stem cells function in homeostasis and tumorigenesis. Extensive new data since the prior review (submitted for publication) establish profound effects of dietary exposures: i) on programming of Lgr5hi and Bmi1+ cells (RNAseq); ii) on capacity for DNA repair in these cells; iii) on subsequent extent, spectrum and signature of mutations that accumulate in cells of these crypt compartments (sequencing of FACS isolated single cells). Aim 1 addresses the hypothesis that dietary induced changes in Lgr5hi stem cell programming, function, and epigenetic alterations can be exceptionally long lived, and therefore that stem cells can be used as “sentinel cells” to monitor the ability of dietary intervention to modulate these alterations as potential markers of risk and targets for intervention. This will provide fundamental data regarding coordination of genes and pathways in regulation of stem cell function, identification of markers of relative risk, and how intervention strategies can be optimized. Aim2 of the initial submission has been largely accomplished, and Aim 2 is revised to investigate the hypothesis that altered DNA repair is important in differential dietary effects on tumorigenesis from the Lgr5+ and Bmi1+ populations when conditional Apc mutations are targeted specifically to each of these cell populations. Aim2 also determines the impact of diet on the nature of mutations in Apc and throughout the genome in the tumors that arise. Aim 3 determines impact of diet on tumor histopathology and programming of tumor epithelial cells when tumors are initiated from either the Lgr5+ or Bmi1+ stem cell compartments. RNAscope and a novel method of transcriptional imaging then determine relative contribution of Lgr5+ and Bmi1+ stem cells to intestinal homeostasis and tumorigenesis under different dietary conditions.