SUMMARY Lineage mapping has identified both proliferative and quiescent intestinal stem cells, but the molecular circuitry controlling stem cell quiescence is incompletely understood. By lineage mapping, we show Lrig1, a pan-ErbB inhibitor, marks predominately non-cycling, long-lived stem cells located at the crypt base that, upon injury, proliferate and divide to replenish damaged crypts. Transcriptome profiling of Lrig1+ colonic stem cells differs markedly from highly proliferative, Lgr5+ colonic stem cells; genes up-regulated in the Lrig1+ population include those involved in cell cycle repression and response to oxidative damage. Loss of Apc in Lrig1+ cells leads to intestinal adenomas and genetic ablation of Lrig1 results in heightened ErbB1-3 expression and duodenal adenomas. These results shed light on the relationship between proliferative and quiescent intestinal stem cells, and support a model in which intestinal stem cell quiescence is maintained by calibrated ErbB signaling with loss of a negative regulator predisposing to neoplasia.

Cellular responses to external stimuli depend on dynamic features of multi-pathway network signaling; thus, the behavior is of a cell is influenced in a complex manner by its environment and by intrinsic properties. Methods of multi-variate systems analysis have provided an understanding of these convoluted effects, but to date this has been only for relatively simplified in vitro cell culture examples. An unaddressed question is whether such approaches can be successfully brought to bear on in vivo conditions. We have analyzed the in vivo signaling network that determines the response of intestinal epithelial cells to the pro-inflammatory cytokine tumor necrosis factor α (TNF-α). We built data-driven, partial least-squares discriminant analysis (PLSDA) models based on signaling, apoptotic, and proliferative responses in the mouse small intestinal epithelium after systemic exposure to TNF-α. We identified the extracellular signal–regulated kinase (ERK) signaling axis as a critical modulator of the temporal variation in apoptosis at different doses of TNF-α, as well as the spatial variation in proliferative responses in distinct intestinal regions. Pharmacologic inhibition of MEK, a mitogen-activated protein kinase kinase upstream of ERK, integrally altered the signaling network and changed the temporal and spatial phenotypes in accordance with a priori model predictions. Our results demonstrate the dynamic, adaptive nature of in vivo signaling networks and identify natural, tissue-level variation in response phenotypes that can be deconvoluted only with quantitative, multi-variate computational modeling. To our knowledge, this is the first study to apply computational modeling of signaling networks to a bona fide in vivo system, and it lays a foundation for the use of systems-based approaches to understand how dysregulation of the cellular network state underlies complex disease.