Transcriptional programming of CD4+ TRM differentiation in viral infection balances effector- and memory-associated gene expression.

After resolution of infection, T cells differentiate into long-lived memory cells that recirculate through secondary lymphoid organs or establish residence in tissues. In contrast to CD8⁺ tissue-resident memory T cells (T_RM), the developmental origins and transcriptional regulation of CD4⁺ T_RM remain largely undefined. Here, we investigated the phenotypic, functional, and transcriptional profiles of CD4⁺ T_RM in the small intestine (SI) responding to acute viral infection, revealing a shared gene expression program and chromatin accessibility profile with circulating T_H1 and the progressive acquisition of a mature T_RM program. Single-cell RNA sequencing identified heterogeneity among established CD4⁺ T_RM, which were predominantly located in the lamina propria, and revealed a population of cells that coexpressed both effector- and memory-associated genes, including the transcriptional regulators Blimp1, Id2, and Bcl6. T_H1-associated Blimp1 and Id2 and T_FH-associated Bcl6 were required for early T_RM formation and development of a mature T_RM population in the SI. These results demonstrate a developmental relationship between T_H1 effector cells and the establishment of early T_RM, as well as highlighted differences in CD4⁺ versus CD8⁺ T_RM populations, providing insights into the mechanisms underlying the origins, differentiation, and persistence of CD4⁺ T_RM in response to viral infection. Committed to memory: Long-lived CD4⁺ tissue resident memory T cells (T_RM) are a crucial component of immune memory, yet their origin and transcriptional regulation are not well understood. Nguyen et al. studied the differentiation of CD4⁺ T cells in the small intestine (SI) after acute LCMV infection. CD4⁺ T_RM cells localized to the lamina propria; were phenotypically, transcriptionally, and epigenetically related to T_H1 cells; and acquired a mature T_RM program over time. A subset of CD4⁺ T_RM co-expressed the antagonistic transcription factors Bcl6 and Blimp1, which, along with Id2, were required to establish T_RM. These findings highlight that CD4⁺ T_RM have a hybrid transcriptional program with expression of effector and memory genes and suggest that in viral infection, circulating T_H1 cells are developmental precursors of SI CD4⁺ T_RM. —HMI [ABSTRACT FROM AUTHOR]