Integrated immune profiling distinguishes polyomavirus nephropathy from rejection phenotypes in kidney allografts

Background: The histologic overlap between polyomavirus-associated nephropathy (PVAN), T-cell–mediated rejection (TCMR), and antibody-mediated rejection (ABMR) creates a major diagnostic challenge. Distinguishing these entities is essential for appropriate management.
We aimed to characterize the immune landscape of renal allografts using integrated immunohistochemical profiling and to determine whether a composite Allograft Immune Landscape Score (AILS) can differentiate PVAN from rejection phenotypes and predict fibrosis progression and graft outcomes.
Methods: A total of 125 biopsies were analyzed, including 40 pure PVAN, 31 PVAN with ABMR, and 54 pure TCMR cases. Integrated immune profiling was performed using five biological domains: immune cell trafficking (CD3, CD8, CD44), macrophage checkpoint signaling (CD68, CD47, SIRPα), innate cytotoxic pathways (CD16, granzyme, perforin), endothelial activation (HLA-DR, C4d, CD47), and tubular immune stress (HLA-DR, CD44, CD47). Each domain was semiquantitatively scored to generate the AILS. Associations between immune markers, interstitial fibrosis (IF), and graft survival were evaluated.
Results: Distinct immune signatures were observed across diagnostic groups. Pure PVAN showed strong tubular CD44 and CD47 expression with moderate macrophage infiltration (p<0.01), consistent with a viral inflammatory niche. Tubular CD47 expression correlated strongly with persistent viremia (p<0.001), and higher macrophage checkpoint scores were significantly associated with the development of IF (p<0.001).
In contrast, PVAN with ABMR demonstrated significantly higher endothelial activation scores, particularly in C4d (+) lesions (p<0.001), characterized by increased PTC HLA-DR expression and C4d deposition. C4d (-) ABMR showed markedly elevated innate effector scores with increased CD16, granzyme, and perforin expression (p<0.01), suggesting NK-cell–mediated antibody-dependent cytotoxicity.
Pure TCMR exhibited the highest immune trafficking and cytotoxic effector scores (p<0.01), reflecting dense CD3⁺/CD8⁺ T-cell infiltration and strong granzyme/perforin expression. CD68 macrophage density correlated significantly with IF severity (p<0.001).
AILS values differed significantly across groups (p<0.001), with the lowest scores in pure PVAN, intermediate scores in TCMR, and the highest scores in PVAN with ABMR, particularly in C4d (+) cases. Higher AILS values were associated with reduced graft survival.
Conclusion: PVAN establishes a tubular inflammatory niche driven by CD44-mediated immune recruitment and macrophage checkpoint signaling via the CD47–SIRPα axis. The interaction between viral injury, macrophage activation, and alloimmune pathways shapes the immune landscape of kidney allografts and influences IF progression and graft outcomes. Integrated immune profiling using AILS may improve diagnostic discrimination between PVAN and rejection phenotypes and help identify patients at risk for progressive graft dysfunction.