STAT4 increases the phenotypic and functional heterogeneity of intestinal tissue-resident memory T cells

Abstract

Tissue-resident memory T cells (Trms) are an important subset of lymphocytes that are lodged within non-lymphoid tissues and carry out diverse functions to control local pathogen replication. CD103 has been used to broadly define subsets of Trms within the intestine, with CD103+ and CD103− subsets having unique transcriptional profiles and effector functions. Here we identify signal transducer and activator of transcription 4 (STAT4) as an important regulator of CD103− Trm differentiation. STAT4-deficient cells trafficked to the intestine and localized to areas of infection but displayed impaired Trm differentiation with fewer CD103− Trms. Single-cell RNA-sequencing demonstrated that STAT4-deficiency led to a reduction in CD103− Trm subsets and expansion of a single population of CD103+ cells. Alterations in Trm populations were due, in part, to STAT4-mediated inhibition of transforming growth factor (TGF)-β-driven expression of Trm signature genes. STAT4-dependent Trm populations expressed genes associated with cytokine production and cell migration, and STAT4-deficient Trm cells had altered localization within the tissue and reduced effector function after reactivation in vivo. Overall, our data indicate that STAT4 leads to increased differentiation of CD103− Trms, in part by modulating the expression of TGF–β-regulated genes, and results in increased Trm heterogeneity and function within the intestinal tissue. Tissue-resident memory T cells (Trms) are an important subset of lymphocytes that are lodged within non-lymphoid tissues and carry out diverse functions to control local pathogen replication. CD103 has been used to broadly define subsets of Trms within the intestine, with CD103+ and CD103− subsets having unique transcriptional profiles and effector functions. Here we identify signal transducer and activator of transcription 4 (STAT4) as an important regulator of CD103− Trm differentiation. STAT4-deficient cells trafficked to the intestine and localized to areas of infection but displayed impaired Trm differentiation with fewer CD103− Trms. Single-cell RNA-sequencing demonstrated that STAT4-deficiency led to a reduction in CD103− Trm subsets and expansion of a single population of CD103+ cells. Alterations in Trm populations were due, in part, to STAT4-mediated inhibition of transforming growth factor (TGF)-β-driven expression of Trm signature genes. STAT4-dependent Trm populations expressed genes associated with cytokine production and cell migration, and STAT4-deficient Trm cells had altered localization within the tissue and reduced effector function after reactivation in vivo. Overall, our data indicate that STAT4 leads to increased differentiation of CD103− Trms, in part by modulating the expression of TGF–β-regulated genes, and results in increased Trm heterogeneity and function within the intestinal tissue.

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