Mesenchymal stem cells orchestrate a hypoxic niche that supports the generation of antigen-specific CD8+ tissue-resident memory T cells in bone marrow after vaccination.

While the role of bone marrow (BM) microenvironment in long-term humoral immunity is well established, its function in vaccine-induced long-term T-cell memory remains poorly understood. Here, we demonstrate that the BM maintains a robust pool of spike-specific CD4+ and CD8+ T cells up to 307 days following inactivated SARS-CoV-2 vaccination. Notably, the frequency of spike-specific CD8+ T cells was significantly higher in the BM than in peripheral blood. Single-cell RNA and TCR sequencing revealed a distinct spike-specific CD8+ tissue-resident memory T (TRM) cell subset within the BM, characterized by a unique transcriptional profile, clonal expansion, and potent cytotoxic potential. Furthermore, we identified that the BM microenvironment is essential for establishing long-term T-cell memory with mesenchymal stem cells (MSCs), providing an important niche for the development of antigen-specific CD8+ TRM cells. Mechanistically, MSCs provide a hypoxic niche and promote the differentiation of CD8+ TRM cells via the HIF1 signaling pathway. Our findings establish the BM as a crucial reservoir for durable T-cell memory induced by vaccination, and uncover a previously underappreciated mechanism of long-term protection centered on a stromal cell-guided, niche-adapted TRM compartment. This work redefines the BM as an active site for the establishment of cellular immune memory after vaccination.