In adult skin, each hair follicle contains a reservoir of stem cells (the bulge), which can be mobilized to regenerate the new follicle with each hair cycle and to reepithelialize epidermis during wound repair. Here we report new methods that permit their clonal analyses and engraftment and demonstrate the two defining features of stem cells, namely self-renewal and multipotency. We also show that, within the bulge, there are two distinct populations, one of which maintains basal lamina contact and temporally precedes the other, which is suprabasal and arises only after the start of the first postnatal hair cycle. This spatial distinction endows them with discrete transcriptional programs, but surprisingly, both populations are growth inhibited in the niche but can self-renew in vitro and make epidermis and hair when grafted. These findings suggest that the niche microenvironment imposes intrinsic "stemness" features without restricting the establishment of epithelial polarity and changes in gene expression.

SUMMARY In adult skin, epithelial hair follicle stem cells (SCs) reside in a quiescent niche and are essential for cyclic bouts of hair growth. Niche architecture becomes pronounced postnatally at the start of the first hair cycle. Whether SCs exist or function earlier is unknown. Here we show that quiescent cells appear early in skin development, express SC markers, and later give rise to the adult SC population. To test whether early quiescent cells function as SCs, we use Sox9-Cre for genetic marking and K14-Cre to embryonically ablate Sox9, an essential adult SC gene. We find that the progeny of Sox9-expressing cells contribute to all skin epithelial lineages and Sox9 is required for SC specification. In the absence of early SCs, hair follicle and sebaceous gland morphogenesis is blocked and epidermal wound repair is compromised. These findings establish the existence of early hair follicle SCs and reveal their physiological importance in tissue morphogenesis.

Summary The body’s first line of defense against environmental assaults, the skin barrier is maintained by epithelial stem cells (EpSCs). Despite EpSCs’ vulnerability to inflammatory pressures, neither the primary response nor its enduring consequences are understood. Here, we unearth a prolonged memory to acute inflammation that enables EpSCs to hasten barrier restoration following subsequent tissue damage. This functional adaptation does not require skin resident macrophages or T cells. Rather, EpSCs maintain chromosomal accessibility at key stress response genes that are activated by the primary stimulus. Upon a secondary challenge, genes governed by these domains are transcribed rapidly. Fueling this memory is Aim2, encoding an activator of the inflammasome. Absence of AIM2 or its downstream effectors, Caspase-1 and Interleukin-1β, erases EpSCs’ ability to recollect inflammation. While EpSCs benefit from inflammatory tuning by heightening their responsiveness to subsequent stressors, this enhanced sensitivity likely increases their susceptibility to autoimmune and hyperproliferative disorders, including cancer.