Biology subjects

Parsa, R.

Publications and source records attributed to Parsa, R..

3 recordsLinked to original sources

bioRxiv2026

Weaning imprints a hybrid cytotoxic-regulatory identity on intestinal CD4+ T lymphocytes

The intestinal immune system must adapt as the neonatal gut shifts from milk to solid food and becomes densely colonized. How the T cell compartment is established under these conditions remains unclear. Using fate-mapping to timestamp naive T cells, with imaging, transcriptomic, and repertoire analyses, we tracked them from suckling to adulthood. Intestinal T cell entry peaked at weaning, coinciding with relocation from crypts to villi guided by the tissue microenvironment and, partly, the microbiota. T cells timestamped at suckling persisted into adulthood and, at weaning, adopted a transient cytotoxic-regulatory state in the lamina propria, with granzyme B expression microbiota-dependent only in the ileum. Clonal expansions at weaning were restricted to the small intestinal lamina propria and absent in germ-free mice. Most expanded clones recognized early-life commensals. Weaning is a physiological window of transient inflammation imprinting a hybrid CD4 T cell compartment, suggesting that early-life commensals modulate T cell selection.

immunology↗

bioRxiv2025

Tissue-specific clonal selection and differentiation of CD4+ T cells during infection

Pathogen-specific CD4 T cells undergo dynamic expansion and contraction during infection, ultimately generating memory clones that shape the subsequent immune responses. However, the influence of distinct tissue environments on the differentiation and clonal selection of polyclonal T cells remains unclear, primarily because of the technical challenges in tracking these cells in vivo. To address this question, we generated Tracking Recently Activated Cell Kinetics (TRACK) mice, a dual-recombinase fate-mapping system that enables precise spatial and temporal labeling of recently activated CD4 T cells. Using TRACK mice during influenza infection, we observed organ-specific clonal selection and transcriptional differentiation in the lungs, mediastinal lymph nodes (medLNs), and spleen. T cell receptor (TCR) sequencing revealed that local antigenic landscapes and clonal identity shape repertoire diversity, resulting in a low clonal overlap between tissues during acute infection. During the effector phase, spleen-derived CD4 T cells preferentially adopted a stem-like migratory phenotype, whereas those activated in the medLNs predominantly differentiated into T follicular helper (Tfh) cells. Memory formation was associated with increased clonal overlap between lung and medLN-derived cells, whereas splenic clones retained a distinct repertoire. Additionally, memory CD4 T cells displayed converging antigen specificity across tissues over time. These results highlight the tissue-dependent mechanisms driving clonal selection and functional specialization during infection and underscore how memory development facilitates clonal redistribution and functional convergence.

immunology↗

bioRxiv2021

Newly recruited intraepithelial Ly6A+CCR9+CD4+ T cells protect against enteric viral infection

The intestinal epithelium comprises the bodys largest surface exposed to viruses. However, a role for intraepithelial T lymphocytes in resistance against viral infections remain elusive. By fate-mapping T cells recruited to the murine intestinal epithelium, we observed accumulation of CD4+ T cells after infection with murine norovirus (MNV) or mouse adenovirus type-2 (AdV), but not after reovirus infection. Intraepithelial CD4+ T cells recruited after MNV or AdV infection co-express Ly6A and CCR9, and exhibit T helper 1 and cytotoxic profiles. Although these cells display a diverse TCR repertoire, they conferred protection against AdV and MNV both in vivo and in an organoid co-culture model in an IFN-{gamma}-dependent manner. Ablation of the T cell receptor (TCR) or the transcription factor ThPOK in CD4+ T cells prior to infection prevented viral control, while TCR ablation during infection did not impact viral clearance. These results uncover a protective role for intraepithelial Ly6A+CCR9+CD4+ T cells against enteric viruses.

immunology↗