Organ-specific features of human kidney lymphatics are disrupted in chronic transplant rejection

Lymphatic vessels maintain tissue fluid homeostasis and modulate inflammation, yet their spatial organisation and molecular identity in the healthy human kidney, and how these change during chronic transplant rejection, remain poorly defined. Here, we show that lymphatic capillaries initiate adjacent to cortical kidney tubules and lack smooth muscle coverage. These vessels exhibit an organ-specific molecular signature, enriched for CCL14, DNASE1L3, and MDK, with limited expression of canonical immune-trafficking markers found in other organ lymphatics, such as LYVE1 and CXCL8. In allografts with chronic mixed rejection, lymphatics become disorganised and infiltrate the medulla, with their endothelial junctions remodelling from a button-like to a continuous, zipper-like architecture. Lymphatics in rejecting kidneys localise around and interconnect tertiary lymphoid structures at different maturation stages, with altered intra- and peri-lymphatic CD4⁺ T cell distribution. The infiltrating T cells express IFNγ, which upregulates co-inhibitory ligands in lymphatic endothelial cells, including PVR and LGALS9. Simultaneously, lymphatics acquire HLA class II expression and exhibit C4d deposition, consistent with alloantibody binding and complement activation. Together, these findings define the spatial and molecular features of human kidney lymphatics, revealing tolerogenic reprogramming, accompanied by structural perturbations, during chronic transplant rejection.