having established that lymphatics are structurally perturbed and spatially associated with immune aggregates in chronic rejection, we next investigated whether lecs in this setting exhibit an altered molecular profile. to do this, we first performed comparative transcriptomic analysis of lecs from healthy kidneys, rejection, and ckd ( supplemental data 5 – 7 ). go revealed that lecs from rejecting allografts were enriched for pathways related to the negative regulation of viral process ( go: 0048525, fold - enrichment = 90. 26, fdr = 5. 95 × 10 ), including ifn - induced transmembrane proteins ifitm2 ( log 2 fc = 1. 76, p = 5. 89 × 10 ) and ifitm3 ( log 2 fc = 1. 62, p = 6. 86 × 10 ) ( figure 7a ). ifn - γ was specifically enriched in t cells and nk cells in our scrna - seq dataset ( figure 7b ), whereas other ifn types were not detected. we then examined an ifn - γ response signature — including levels of ifitm2, ifitm3, and the ifn - γ receptor subunits ifngr1 and ifngr2 — which was prominent in lecs and in blood endothelial cells and macrophages from rejecting allografts ( figure 7c ). to contextualize this response, we compared the lec profile in chronic rejection with that of hevs, identified by enrichment for pnad ( ntan1 ) and downregulation of notch pathway genes rbpj and jag1 ( supplemental figure 5b ) ( 83, 84 ). unlike lecs, hevs lacked lymphatic markers prox1 and pdpn ( supplemental figure 5c ). instead, they expressed transcripts involved in leukocyte recruitment, activation, and regulation, such as cxcl16, fractalkine ( cx3cl1 ), cd40, and il - 32 ( supplemental figure 5d and supplemental data 8 ), highlighting a distinc t immune regulatory profile compared with lecs. we next explored potential ligand - receptor interactions between lecs and lymphocytes using cellphonedb ( 85 ). predicted cell - cell communication was highest in rejecting kidneys compared with ckd or healthy controls ( supplemental figure 6a ), with most interactions occurring between lecs and t cell subsets ( supplemental figure 6b ). these included ifn - γ – ifngr signaling from cd8 t cells to lecs across both control and rejecting kidneys ( supplemental figure 6c ). chemok ine - based interactions included established axes such as ccl21, ccl2, and ackr2 ( supplemental figure 7a ), although ccl14 / ackr2 signaling with cd4 effector t cells was reduced in rejection. many chemok ine receptors for ackr2 ligands, including ccr2, ccr5, and ccr7, were expressed by t cells ( supplemental figure 7b ). notably, most of the remaining predicted interactions were coinhibitory in nature. these included lec expression of poliovirus receptor ( pvr ) and galectin 9 ( lgals9 ), which suppress effector t cell responses via tigit and havcr2 signaling, respectively ( 86 ) ( figure 7d ). while also present in ckd and non - alloimmune graft injury ( supplemental figure 8, a – c ), these interactions had higher signaling scores in chronic rejection ( figure 7e ). immunostaining confirmed pvr expression on pdpn lymphatics in direct contact with cd4 t cells in rejecting allografts ( figure 7f ). when stimulated by ifn - γ, blood endothelia express pvr and lgals9 to dampen t cell responses ( 87, 88 ). to examine whether this was the case for lecs, we stimulated a human lec line with recombinant ifn - γ. lgals9 transcripts were significantly upregulated after 24 hours ( mean fc = 9. 05, 95 % ci = 5. 37 – 12. 73, adjusted p = 0. 0002 ) and remained elevated at 48 hours ( mean fc = 5. 10, 95 % ci = 1. 42 – 8. 78, adjusted p = 0. 0093 ) ( figure 7g ). corresponding increases in lec - secreted lgals9 protein were observed at 48 hours ( difference in mean concentratio n = 5. 54 ng / ml, 95 % ci = 3. 26 – 7. 83, adjusted p = 0. 0002 ) and 72 hours ( difference in mean concentratio n = 16. 87 ng / ml, 95 % ci = 14. 58 – 19. 16, adjusted p < 0. 0001 ) ( figure 7h ), confirming that lecs can acquire a coinhibitory profile in response to ifn - γ exposure. however, in solid organ transplantation, ifn - γ – induced expression of hlas on endothelial cells can facilitate alloantigen presentation and antibod y binding to donor vasculature ( 89, 90 ). similarly, we found rejected allograft lecs also expressed hla - dp and hla - dr ( figure 8a ). to determine whether lymphatics were of donor or recipient origin, we assessed genotype using single-nucleotide variant calling, and found a majority of lecs were donor derived, with a small recipient cell contribution ( n = 3 / 247, 1. 2 % ) ( figure 8b ), consistent with a previous study of sex - mismatched renal allografts ( 91 ). immunostaining for hla - dr in chronic rejection ( figure 8c ) demonstrated its expression on cd31 blood endothelial cells ( figure 8d ), cd68 macrophages ( figure 8e ) ( 92, 93 ), and pdpn lymphatics ( figure 8, f and g ). importantly, we detected complement factor c4d deposition, a histological hallmark of allo antibod y - mediated complement activation, on pdpn lymphatic vessels in 2 rejecting allografts from patients with de novo donor - specific antibod ies ( figure 8h ). these hla - dr lymphatic regions were surrounded by cd3 t cells ( supplemental video 10 ), suggesting coordinated allo antibod y and t cell engagement. together, these data demonstrate that lecs in chronic rejection acquire an ifn - γ – responsive, immune - inhibitory transcriptional phenotype, marked by coinhibitory ligand expression, hla class ii upregulation, and evidence of complement activation. lymphatic vessels play a central role in maintaining fluid balance and immune homeostasis, yet their structural and molecular features in the human kidney remain underexplored. this gap is clinically relevant, as lymphangiogenesis occurs across a range of kidney diseases ( 11 – 14 ), and augmenting lymphatic function confers therapeutic benefit in preclinical models of kidney disease ( 94 – 96 ), hypertension ( 97 – 99 ), and acute kidney transplant rejection ( 29 ). here, we combined 3d imaging of optically cleared tissue with scrna - seq to resolve the spatial architecture and molecular identity of lymphatics in the healthy human kidney and to interrogate their remodeling in chronic transplant rejection. although previous studies have identified lymphatics in the kidney hilum and cortex ( 11 – 14 ), our 3d imaging approach yielded potentially new spatial insights, including a hierarchical arrangement of kidney lymphatics and the initiation of blind ends near proximal and distal tubular nephron segments, key sites of reabsorption and solute exchange between the urinary filtrate and blood. using scrna - seq, we defined a transcriptional census of human kidney lecs, identifying expression of molecules previously characterized in other lymphatic beds but not in human kidney lecs, such as fabp4 ( 100, 101 ) and angpt2 ( 102 – 104 ). a recent analysis has transcriptionally profiled a population of lecs in the lymph node ( 105 ). our findings further extend the evidence for organ - specific heterogeneity of human lymphatics. compared with lymphatics from barrier tissues such as skin, lung, and intestines, kidney lecs displayed reduced expression of genes encoding classical immune trafficking molecules like cxcl8 and lyve1, the latter confirmed at the protein level and also recently corroborated in mouse kidneys ( 106 ). instead, kidney lecs express a repertoire of other molecules, including dnase1l3, a molecule involved in extracellular dna clearance and deficiency of which is implicated in lupus nephritis ( 107 – 109 ). such findings could suggest tissue - specific adaptations of the lymphatic regulation of immunity and may inform future studies of immune-mediated kidney disease. although lymphatic valve markers were sparsely detected, unlike in mouse kidneys ( 110 ), we identified transcriptional heterogeneity among kidney lecs, including a subpopulation enriched for ccl2 and cxcl2.