Kusch, A. | bioRxiv Science

bioRxiv2026

Spatial remodeling of the thymic stroma with age disrupts niches for T cell selection and tolerance

Age-associated thymic involution is a major driver of immunosenescence, yet the cellular and spatial mechanisms coordinating age-related thymic remodeling remain incompletely understood. Combining single-cell transcriptomics, chromatin accessibility profiling, and spatial transcriptomics, we generated a spatially resolved multi-omic atlas of the aging mouse thymus. We show that thymic aging is not simply a process of epithelial loss, but a spatial reorganization of the stroma into new microenvironments, including age-associated epithelial states, a fibroblast-supported epithelial progenitor niche, and tertiary lymphoid structures. This remodeling displaces niches supporting positive and negative thymocyte selection and coincides with an intrinsic decline in cortical thymic epithelial cell function. Ligand-receptor mapping identifies medullary fibroblasts as a signaling hub sustaining epithelial progenitors and promoting tertiary lymphoid structure neogenesis, linking these hallmarks of thymic aging. Together, our findings reframe thymic involution as spatial stromal reorganization that links stromal remodeling to impaired thymopoiesis, central tolerance, and immune aging.

immunology↗

bioRxiv2025

Ly6d expression delineates two putative postnatal thymus epithelial progenitor cells that are differentially affected by ageing

The thymus is a primary lymphoid organ which provides essential structural and functional support for the development of naive T cells. Thymic epithelial cells (TECs), key components of the thymic stroma, are classified into cortical (cTEC) and medullary (mTEC) lineages based on their distinct molecular, structural, transcriptional, and functional characteristics. Advances in single-cell RNA sequencing (scRNA-seq) have revealed significant TEC heterogeneity, including the identification of intertypical TECs that share properties of both cTEC and mTEC and have been postulated to play a role in the development and maintenance of thymic function. To date, the identity and maintenance of postnatal TEPCs remain unclear, with debates on whether bipotent TEPCs persist after birth or if lineage-restricted progenitors independently maintain TEC compartments. Using an inducible lineage-tracing system based on {beta}5t expression, we explored the early dynamics of the relationships between TEPC and mTEC progenitors and their progeny. Our results identified two potential lineage-biassed TEPC subpopulations, distinguished by Ly6d expression. Additionally, we observed that ageing disproportionately affects Ly6d-compared to Ly6d+ TEPCs, with implications for the rejuvenation of the ageing thymic epithelium. This study provides insights into the developmental pathways of TEC lineages and their maintenance, contributing to strategies for enhancing thymic function in ageing and disease.

immunology↗