Compartmentalization of Transcripts During Antibody Mediated Rejection in Renal Transplants

We used Digital Spatial Profiling to localize transcripts in glomeruli and tubulointerstitial compartments in a series of 4 biopsies from a patient diagnosed with acute antibody-mediated rejection (AMR). The 4 biopsies included: a baseline protocol biopsy 25 days after transplantation; a 3 month biopsy diagnosed as acute AMR; a biopsy 4 months after treatment with intravenous immunoglobulin (IVIg) showing ongoing AMR with a mild increase in tubulointerstitial fibrosis; and a biopsy 7 months later with resolution of glomerulitis. Glomeruli were captured in regions of interest (ROIs) for whole exome sequencing. Compared to baseline glomeruli, 17 transcripts were increased and 39 decreased in the 3 subsequent biopsies (> 2-fold and p < 0.005). Increased signatures for macrophages correlated with increased numbers of CD68 positive cells imaged in the corresponding glomeruli. The Human Cell Atlas classified the 39 transcripts decreased during the initial rejection as characteristic of podocytes and this gene signature did not recover in the subsequent 2 biopsies. Additional ROIs encompassing areas of tubulointerstitial fibrosis disclosed signatures for memory B cells in the acute AMR sample. Treatment with IVIg did not eliminate the B cell signal in the subsequent biopsy. Collectively these data demonstrate a compartmentalization of injury processes. Innate immune cells including macrophages were located in glomerular and tubulointerstitial compartments, whereas, adaptive immune cells including memory B cells localized to the tubulointerstitial compartment. Furthermore, podocyte transcripts were decreased in glomeruli and did not recover with treatment indicating a vulnerability of these cells to acute AMR.