Tissue resident memory CD4 ⁺ T cells are sustained by site-specific levels of self-renewal and continuous replacement

Tissue-resident memory T cells (T _RM ) protect from repeat infections within organs and barrier sites. The breadth and duration of such protection is defined at minimum by three quantities; the rate at which new T _RM are generated from precursors, their rate of self-renewal, and their rate of loss through death, egress, or differentiation. Quanti-fying these processes individually is challenging. Here we combine genetic fate mapping tools and mathematical models to untangle these basic homeostatic properties of CD4 ⁺ T _RM in the skin and gut lamina propria (LP) of healthy adult mice. We show that CD69 ⁺ CD4 ⁺ T _RM in skin reside for ∼24 days and self-renew more slowly, such that clones halve in size approximately every 5 weeks; and approximately 2% of cells are replaced daily from precursors. CD69 ⁺ CD4 ⁺ T _RM in LP have shorter residencies (∼14 days) and are maintained largely by immigration (4-6% per day). We also find evidence that the continuous replacement of CD69 ⁺ CD4 ⁺ T _RM at both sites derives from circulating effector-memory CD4 ⁺ T cells, in skin possibly via a local CD69 ^- intermediate. Our approach maps the ontogeny of CD4 ⁺ T _RM in skin and LP and exposes their dynamic and distinct behaviours, with continuous seeding and erosion potentially impacting the duration of immunity at these sites.