Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury

The currently accepted intestinal epithelial cell organization model proposes that crypt base columnar (CBC) cells marked by high levels of Lgr5 expression represent the sole intestinal stem cell (ISC) compartment. However, previous studies have indicated that Lgr5+ cells are dispensable for intestinal regeneration, leading to two major hypotheses: one favoring the presence of a quiescent reserve stem cell population, the other calling for differentiated cell plasticity. To investigate these possibilities, we studied crypt epithelial cell organization, during homeostasis and regeneration, in unbiased fashion, via high-resolution single-cell profiling. These studies, combined with in vivo lineage tracing, show that Lgr5 is not a specific ISC marker and that stemness potential exists beyond the crypt base in the isthmus region, whose cells, contrary to differentiated cells, participate in tissue homeostasis and support intestinal regeneration. Our results provide a novel model of organization for the intestinal crypt epithelium in which stemness potential is not restricted to CBC cells and suggesting that neither de-differentiation nor reserve stem cell populations are drivers of intestinal regeneration. ### Competing Interest Statement Dr. Califano is founder, equity holder, and consultant of DarwinHealth Inc., a company that has licensed some of the algorithms used in this manuscript from Columbia University. Columbia University is also an equity holder in DarwinHealth Inc. US patent number 10,790,040 has been awarded related to this work, and has been assigned to Columbia University with Dr. Califano as an inventor.