Unveiling Spatial Immune Cell Profile in Kidney Allograft Rejections Using 36-plex Immunofluorescence Imaging

Abstract

Background. Kidney allograft rejections are orchestrated by a variety of immune cells. Because of the complex histopathologic features, accurate pathological diagnosis poses challenges even for expert pathologists. The objective of this study was to unveil novel spatial indices associated with transplant rejection by using a spatial bioinformatic approach using 36-plex immunofluorescence image data. Methods. The image obtained from 11 T cell-mediated rejection (TCMR) and 12 antibody-mediated rejection (AMR) samples were segmented into 753 737 single cells using DeepCell’s Mesmer algorithm. These cells were categorized into 13 distinct cell types through unsupervised clustering based on their biomarker expression profiles. Cell neighborhood analysis allowed us to stratify kidney tissue into 8 distinct neighborhood components consisting of unique cell type enrichment profiles. Results. In contrast to TCMR samples, AMR samples exhibited a higher frequency of neighborhood components that were characterized by an enrichment of CD31+ endothelial cells. Although the overall frequency of CD68+ macrophages in AMR samples was not significantly high, CD68+ macrophages within endothelial cell-rich lesions exhibited a significantly higher frequency in AMR samples than TCMR samples. Furthermore, the frequency of interactions between CD31+ cells and CD68+ cells was significantly increased in AMR samples, implying the pivotal role of macrophages in AMR pathogenesis. Importantly, patients demonstrating a high frequency of CD31:CD68 interactions experienced significantly poorer outcomes in terms of chronic AMR progression. Conclusions. Collectively, these data indicate the potential of spatial bioinformatic as a valuable tool for aiding in pathological diagnosis and for uncovering new insights into the mechanisms underlying transplant rejection.