Spatial Analysis Identifies Endothelial HLA-F as a Prognostic Marker in Antibody-mediated Rejection

Background. Microvascular injury (MVI) is a key histopathological feature required for the diagnosis of antibody-mediated rejection (ABMR) in kidney allografts. However, MVI alone is insufficient for definitive diagnosis or accurate prognostication. We previously demonstrated that interactions between cluster of differentiation 31 (CD31) + endothelial cells and cluster of differentiation 68 (CD68) + macrophages within the peritubular capillary (PTC) niche are associated with graft outcome. To further elucidate the molecular mechanisms underlying this cellular interplay, we performed spatial transcriptomic profiling focused on the PTCs niche using the GeoMx Digital Spatial Profiler. Methods. This study was conducted in 2 phases. In the discovery cohort, total RNA was extracted from CD31 + and CD68 + regions within the PTC niche from 3 ABMR and 3 T cell–mediated rejection (TCMR) samples, followed by sequencing using the whole-transcriptome atlas (WTA; >18 000 genes). For validation, 67 kidney allograft biopsy samples (42 ABMR and 25 non-ABMR) were analyzed by immunohistochemistry (IHC) for HLA-F, identified as a candidate spatial signature of ABMR in the PTC niche. Results. Preranked gene set enrichment analysis revealed a coordinated interferon-γ-driven transcriptional program across both CD31 + and CD68 + compartments in ABMR, with HLA-F emerging as a prominent feature. HLA-F expression was significantly associated with MVI severity and donor-specific antibody positivity. Among patients with active ABMR, higher HLA-F expression was associated with a greater decline in kidney function following biopsy. Conclusion. These findings identify HLA-F as a novel molecular marker linked to ABMR pathogenesis and prognosis, highlighting its potential utility as a spatially resolved biomarker within the PTC niche.