therefore, cmv infection drives t cell gene signature changes that overlap with, but are distinc t from, age - related immune alterations. cd4 t cells are highly heterogeneous and exhibit functional and phenotypic continuums, suggesting that age effects could differentially manifest within or across subsets. we applied an annotation - independent analysis of aging in cd4 t cells in the lung, jej and ln, leveraging a per - cell estimation of age effects using counterfactual analysis with mrvi, which separately considers each cell and controls for covariates. this analysis identified groups of cells with similar predicted age - associated changes in gene expression ( ‘ modules ’ ), which we interrogate d by de analysis across age ( fig. 7, extended data fig. 6, and supplementary tables 23 and 24 ). in the lung, a fraction of cd4 t cells ( ~ 25 %, comprising t em cells, t rm cells and t emra cells ) exhibited decreased cytotoxicity ( gzmh, gnly, gzma ) and increased cytokine receptor ( il18r1, ifngr1 ) genes with age ( fig. 7a – c and extended data fig. 6a, b ). similar upregulation of cytokine responsiveness with age occurred in some cd4 t cells in blood, bm, ln and spleen, while decreased cytotoxicity was unique to the lungs ( fig. 7c, d and extended data fig. 6b ). cd4 t cells in the jej ( mainly t rm cells ) exhibited an age - related decline in t h 17 - associated genes ( il17a, il17f, il22, rorc, ccr6 ) and increase in pro - inflammatory cytokines ( ifng, tnf ) ( fig. 7e – g and extended data fig. 6c, d ); age - associated downregulation of il - 17 - associated genes was also observed in cd4 t cells in lung and blood ( fig. 7g – h and extended data fig. 6d ). cd4 t cells in the ln ( also in spleen and lungs ) exhibited reduced expression of genes associated with regulation ( il10, tigit, ctla4, cd27 ) and increased expression of inflammation and activation markers ( il18bp, tnfrsf4, tnf ) with age ( fig. 7i – l and extended data fig. 6e, f ). these results revealed age - associated transcriptional changes in tissue cd4 t cells associated with site - specific functions. we present a comprehensive analysis of the human immune system across tissues and ages through multimodal profiling of blood and tissues from organ donors spanning six decades of adult life. we found that tissue localization was a dominant driver of the immune landscape, determining immune cell composition, cell states and functional capacity. with age, these tissue - specific properties were largely maintained, although certain subsets and sites showed altered function, migration and regulation. our results reveal that the human immune system is highly specialized for diverse tissue environments to maintain homeostasis and mount effective immune responses. we demonstrated that each tissue imposed site - specific immune cell compositions and adaptations that varied by lineage, and these tissue effects were conserved across donors. although we realized and reinforced site - specific features for t rm cells at barrier sites and lymphoid organs, whether these adaptations applied to other immune cells remained unknown. here, we found that site - specific signatures for t cells in the gut ( high tissue residency, low cytotoxicity ), lungs ( high effector function, increased regulation ) and lymphoid organs ( stem - like features ) were not exclusive to the canonical resident populations, were shared across nk cell and ilc subsets and were absent from b cell and myeloid lineages. the enhanced expression of stem - like transcription factors tcf - 1 and lef - 1 by ln memory t cells suggests that lymphoid organs may serve as reservoirs for long - lived memory cells, given these factors ’ requirement for memory t cell generation. macrophages and plasma cells also exhibited site - specific features in the gut, lungs and lymphoid organs through distinc t subset - specific pathways, such as alveol ar macrophages in the lungs and red pulp macrophages in the spleen. these lineage - dependent tissue adaptations probably reflect niche localization and interactions with distinc t structural and immune cells within each tissue. age - associated gene signatures identified for macrophages, t cells and b cells were intrinsic to the subset and site. the apoe – trem2 gene signature, essential for crucial macrophage functions, was reduced with age by lung macrophages. apoe – trem2 expression in microglia is associated with neurodegeneration in alzheimer ’ s disease and in other macrophage types with cardiov ascular diseases. trem2 can have different effects on macrophage functions; promoting anti-inflammatory ‘ m2 - like ’ function in some contexts and phagocytosis and sustained inflammation in others. the age - associated loss of trem2 in lung macrophages could thus account for compromised immunity to respiratory pathogens and increased lung cancer susceptibility observed in the aging population. trem agonists that enhance phagocytic function are being tested in clinical trials in alzheimer ’ s disease and could be considered in the rejuvenation of aging macrophages in other sites. other age - associated features were specific to lymphocyte lineages. t cells in circulation expressed higher levels of genes associated with inflammation, cytotoxicity and nk - like markers with age, as previously reported. circulating t emra cells and t em cells upregulated gzmk and other markers, similar to senescent gzmk cd8 t cells found in mice and human blood. t rm cells in the lungs and intestines did not exhibit this age - associated gene signature, suggesting that the tissue environment may insulate them from signals that promote cellular aging or that cellular aging is tissue - specific. however, both circulating ( t em, t emra ) and t rm cells had increased expression of genes for pro - inflammatory cytokines and chemok ines with age, consistent with inflammaging implicated in cardiov ascular diseases and metabolic dysregulation. our findings suggest that human t cells may be more prone to innate functions such as cytokine - driven activation ( for example, via il - 18 ) with age. we also identified an age - associated increase in il - 18 expression and reduced bcr - mediated signaling within tissue b cells, which is a feature of nk - like b cell subsets identified in disease contexts. thus, aging may reflect a broader age - related shift to innate - like functions in both t cells and b cells. our findings have important implications for immune monitoring, therapeutic modulation and clinical advancement. the compartmentalization of immune subsets across tissues emphasizes the importance of site - specific immune monitoring in disease states, as exemplified in severe covid - 19, in which immune dynamics in the respiratory tract rather than blood correlated with infection outcome. the distinc tness of gut - specific subsets provides rationale for targeted intestinal interventions, as demonstrated by rotavirus vaccines. the identification of stem - like profiles ( marked by tcf7 and lef1 expression ) in ln t cells and nk cells has direct relevance to adoptive car - t immunotherap ies, in which stemness is associated with remission. lns may thus represent an optimal source of nk and t cells for engineering adoptive cell therapies against cancer, infections and autoimmunity. our study has several limitations. the low frequency of certain immune subsets in tissues, including dcs, macrophages in lymphoid organs and hematopoietic progenitors, precluded aging analysis and will require sorting for future studies. similarly, an in - depth analysis of tcr and bcr across sites and age would require isolating memory t cells and b cells from each site. finally, although we identified age - associated changes in 24 donors, additional donors would increase power and probably reveal additional aging signatures.