we integrated data in a semi - supervised manner using scanvi, where skin cell types were labeled and cells from other tissues were unlabeled. we used the same scanvi hyperparameter s as for wound data but with a smaller number of maximum epochs ( n = 10 ) due to the larger dataset size. we then calculated k - nn ( k = 30 ) and performed low - resolution leiden clustering ( resolution 0. 1 ). we selected a fibroblast cluster based on canonical marker genes, which also contained the labeled skin fibroblasts. to annotate clusters, we labeled clusters by the majority skin fibroblast population ( fig. 6c and extended data fig. 8b ) ( for example if f3: frc - like was the predominant skin fibroblast subtype, we labeled the cluster as f3: frc - like ). we then assessed gene expression markers for each cluster, excluding skin fibroblasts, to ensure that skin fibroblasts did not drive the gene expression signature for that cluster. we also plotted gene expression for each cluster by tissue using our previously reported marker genes for each cluster. to assess f3: frc - like fibroblasts in hlca data, we performed the same clustering strategy as previously described for skin fibroblasts and then plotted f3: frc - like marker genes by cluster. inflammation severity scores were obtained from geo under accession code gse282122. a linear regression model was fitted using ordinary least squares with the f6 proportion as the dependent variable and inflammation severity score as the independent variable using seaborn ’ s regplot function. we used cellphonedb v. 5 ( method 2 ) for cell – cell communication analysis. we combined our fibroblast data with skin immune cells from our previously published scrna - seq data from skin with more granular immune cell annotations ( reynold s et al. ). we restricted interactions to marker genes for f3: frc - like fibroblasts and f6: inflammatory myof ibroblasts. we visualized the results using ktplotspy. for prenatal skin and prenatal intestine, we concatenated raw count adata objects from intestine with our prenatal skin data from a previous publication. we ran scvi using the same parameters as for the healthy / nonlesional integration. we used the same strategy for the adult skin and prenatal skin integration. for mouse comparisons, we downloaded the mouse steady-state atlas from https: / / www. fibroxplorer. com / download. we loaded the data as an adata object using pandas2ri in rpy2. we used labels for ccl19 fibroblast from the original study. further information on research design is available in the nature portfol io reporting summary linked to this article. any methods, additional references, nature portfol io reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at 10. 1038 / s41590 - 025 - 02267 - 8. organ - specific features of human kidney lymphatics are disrup ted in chronic transplant rejection source paper: pmc12435838 lymphatic vessels maintain tissue fluid homeostasis and modulate inflammation, yet their spatial organization 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 disor ganized and infiltrate the medulla, with their endothelial junctions remodeling from a button - like to a continuous, zipper - like, architecture. lymphatics in rejecting kidneys localize around and interconnect tertiary lymphoid structures at different maturation stages, with altered intralymphatic and perilymphatic cd4 t cell distribution. the infiltrating t cells express ifn - γ, which upregulates coinhibitory ligands in lymphatic endothelial cells, including pvr and lgals9. simultaneously, lymphatics acquire hla class ii expression and exhibit c4d deposition, consistent with allo antibod y 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. lymphatics are blind - ended vessels lined by lymphatic endothelial cells ( lecs ); they are responsible for clearing fluid and macromolecules from the microenvironment and play a critical role in maintaining tissue homeostasis ( 1 – 3 ). during inflammation, lymphatics expand through lymphangiogenesis to facilitate leukocyte efflux. while their role and therapeutic potential in lymphedema ( 4 ), cardiov ascular disease ( 5 – 7 ), cancer ( 8 ), and neuropathology or neuroinflammation ( 9, 10 ) are becoming increasingly recognized, these functions rely on organ - specific structural and molecular specialization. in the kidney, lymphatic vasculature is considered an important entity in physiology and disease ( 11 – 14 ). epithelial nephrons and their associated blood capillary networks ( 15 ) underlie plasma ultrafiltration, fluid homeostasis, and acid - base balance. in contrast, although lymphatics appear in the human fetal kidney by the end of the first trimester ( 16 ), their precise spatial organization, molecular identity, and cellular interactions remain poorly defined. kidney transplantation, the most common solid organ transplant, has excellent short - term outcomes but is limited long - term by chronic rejection, a major cause of late allograft failure ( 17, 18 ). chronic rejection, driven by both t cell – mediated injury and / or donor - specific antibod ies targeting hla, results in microvascular injury, interstitial fibrosis, and tubular atrophy ( 19, 20 ). lymphatics serve as a route for trafficking of antigens and leukocytes, but their role in transplant immunity remains controversial ( 11, 21, 22 ). lymphangiogenesis in kidney transplants ( 23 – 26 ) has been associated with promoting resolution of inflammation and improving allograft function ( 27 – 29 ) but also with alloantigen presentation and fibrosis ( 30, 31 ). these contrasting findings underscore the need to better understand lymphatic remodeling in transplant rejection and how it diverges from other kidney pathologies featuring lymphangiogenesis ( 32 – 34 ). here, we used 3d microscopy of optically cleared and immunolabeled tissue, in addition to single - cell rna - seq ( scrna - seq ), to map the spatial organization and molecular profile of lymphatics in the healthy human kidney. we identified blind - ended lymphatic capillaries around cortical nephron segments, with a distinc t molecular signature compared with lecs from other organs. in allografts with chronic mixed rejection, lymphatic vessels expanded into the medulla and were structurally disor ganized, with disrup ted lec - cell junctions. in this setting, lymphatics surrounded tertiary lymphoid structures, with altered intralymphatic and perilymphatic cd4 t cell distribution. however, our molecular analyses suggest that lecs are tolerogenic and respond to t cell – derived ifn - γ by upregulating immune - inhibitory molecules. critically, lymphatics in rejecting allografts also expressed hla class ii and exhibited complement 4d ( c4d ) deposition, indicative of allo antibod y binding ( 35 ). thus, our findings revealed that kidney lymphatics in chronic rejection adopt potentially compensatory tolerogenic changes but are concurrently structurally perturbed, better defining their contributions to alloimmunity.