Spatial Transcriptomic Signatures of Early Acute T Cell–mediated Rejection in Kidney Transplants

Abstract

Background. Kidney transplantation significantly improves the quality of life for those with end-stage renal failure, yet allograft rejection resulting from immune cell interactions remains a persistent challenge. Although T cell–directed immunosuppressive drugs effectively contain graft rejection in most patients, a notable proportion still experiences acute T cell–mediated rejection (TCMR). Despite an emphasis on suppressing T cell–mediated immune responses, successful control over TCMR is not always achieved, suggesting the potential involvement of factors beyond T cells. Methods. Biopsy samples from suspicious (borderline) for acute TCMR (borderline TCMR) and non-TCMR patients were obtained 9 d postsurgery, and spatial transcriptomics profiling was conducted using the GeoMx Digital Spatial Profiler platform. Regions of interest in the glomerulus and interstitium were selected on the basis of immunohistochemistry staining anti-CD3 to identify areas with T-lymphocyte infiltration. Differential gene expression analysis was performed using unpaired t tests. Results. Unbiased clustering of transcriptional profiles across all regions of interest showed distinct transcriptional profiles between glomeruli and interstitium in non-TCMR samples, whereas borderline TCMR samples displayed no distinct transcriptional profiles between these regions. Contrary to the prevailing T cell–centric view, we observed pathways and genes associated with innate immunity-related inflammatory conditions expressed in glomerular regions of borderline TCMR biopsies. Immunofluorescence staining for CD68 confirmed the presence of macrophages in the glomeruli of the post-TCMR sample in a validation cohort, indicating macrophage involvement in the glomerular response after TCMR. Conclusions. Activation of the innate immune response in borderline TCMR appears to impact not only the interstitium but also the glomerulus. Glomerulus-specific immune signatures suggest the role of the innate immune system in rejection. This nuanced understanding proposes the necessity for tailored therapeutic interventions targeting both innate and adaptive immune pathways to enhance transplant outcomes.