Spatiotemporal Single-cell Profiling Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease

Recent work published in Nature Immunology suggests that donor T cell clones that drive severe graft-versus-host disease (GVHD) can be fingerprinted before transplant, tracked in blood for two years, and located in the gut near intestinal crypts they destroy. Led by researchers at Columbia University in New York, the study nominates early repertoire dynamics and the spatial burden of effector hubs as candidate biomarkers.

Acute GVHD remains the chief barrier to allogeneic hematopoietic cell transplantation (alloHCT), yet how donor CD8⁺ T cells acquire tissue-resident phenotypes and reach vulnerable epithelial niches has not been mapped in humans. The investigators defined alloreactive clones before transplant using mixed lymphocyte reaction (MLR) fingerprinting with T cell receptor beta (TCRβ) sequencing, then followed them longitudinally in blood. Gut biopsies were profiled by paired single-cell RNA sequencing and TCR sequencing of separated lamina propria (LP) and intraepithelial (IE) compartments.

Across 31 individuals and 2 normal donors, 57,062 alloreactive clones were identified across 25 MLRs. Severe GVHD showed persistently higher cumulative alloreactive frequencies at every interval across the first year (P < 0.05) and more expanded clones beyond day 68. In tissue, CD8⁺ effector and proliferating T cells were enriched in severe GVHD (P < 0.05, n = 14/10/14 samples), while mild disease was dominated by CD4⁺ effectors. Mobile clones migrating from LP to IE converted into Hobit (ZNF683)⁺PRDM1⁺ tissue-resident memory cells (P = 1.865 × 10⁻³⁰ in severe disease). Spatially, CD8⁺ effector hub abundance correlated inversely with distance to intestinal stem cells (r = −0.89, P = 0.003), and these cells accumulated in crypt-loss regions where stem cells were depleted (P < 0.0001). Together these data trace a continuous route from a pretransplant alloreactive fingerprint through early clonal expansion in blood to a crypt-adjacent resident effector population, suggesting that both the blood repertoire in the first weeks and the tissue burden of CD8⁺ effector hubs could be read as early indicators of who is heading toward severe gut GVHD.

Reference

Shi L, Uzuni A, Wang XK, et al. Spatiotemporal single-cell profiling reveals T cell clonal dynamics and phenotypic plasticity in human graft-versus-host disease. Nat Immunol. 2026;27(10):2156-2171. https:/doi.org/10.1038/s41590-026-02631-2