Transcriptional and spatial profiling of the kidney allograft unravels a central role for FcyRIII+ innate immune cells in rejection

Abstract

Rejection remains the main cause of premature graft loss after kidney transplantation, despite the use of potent immunosuppression. This highlights the need to better understand the composition and the cell-to-cell interactions of the alloreactive inflammatory infiltrate. Here, we performed droplet-based single-cell RNA sequencing of 35,152 transcriptomes from 16 kidney transplant biopsies with varying phenotypes and severities of rejection and without rejection, and identified cell-type specific gene expression signatures for deconvolution of bulk tissue. A specific association was identified between recipient-derived FCGR3A+ monocytes, FCGR3A+ NK cells and the severity of intragraft inflammation. Activated FCGR3A+ monocytes overexpressed CD47 and LILR genes and increased paracrine signaling pathways promoting T cell infiltration. FCGR3A+ NK cells overexpressed FCRL3, suggesting that antibody-dependent cytotoxicity is a central mechanism of NK-cell mediated graft injury. Multiplexed immunofluorescence using 38 markers on 18 independent biopsy slides confirmed this role of FcγRIII+ NK and FcγRIII+ nonclassical monocytes in antibody-mediated rejection, with specificity to the glomerular area. These results highlight the central involvement of innate immune cells in the pathogenesis of allograft rejection and identify several potential therapeutic targets that might improve allograft longevity.

Renal cell classification in highly multiplexed microscopy imaging using a biology-based decision tree classifier

“…Conversely, we see an enrichment of myeloid cells in our lupus nephritis cohorts indicated by 2). This observed pattern matches known immune populations commonly reported in both diseases 5,6 . Since cells in our UMAP plots matched the expected and desired cell behaviors reported in human disease literature, we can be more confident that our algorithm is performing as intended.…”

RNA-sequencing of Human Kidney Allografts and Delineation of T-Cell Genes, Gene Sets, and Pathways Associated With Acute T Cell–mediated Rejection

“…We used 2 signature matrices—the LM22 signature derived from peripheral blood mononuclear cells 38 and the KTB18 signature derived from single-cell sequencing of kidney allografts. 39 The absolute scores of CD4 memory T cells, CD8 T cells, Treg, and Tfh were significantly higher in TCMR versus NR biopsies using the LM22 signature matrix (Figure 9A). The absolute scores of CD4 naive cells, CD4 memory T cells, CD8 effector cells, and CD8 TEMRA were significantly higher using the KTB18 signature matrix (Figure 9B).…”

“…Fractions in each biopsy is shown in the box plots. B, the KTB18 signature matrix derived from single-cell RNA-Seq of kidney allografts 39 was applied as the reference base matrix for deconvolution. The fractions of T-cell subsets included in the KTB18 signature matrix that were significantly different between TCMR biopsies and NR biopsies are shown.…”

SOX9 switch links regeneration to fibrosis at the single-cell level in mammalian kidneys

“…To obtain single-cell-level resolution of the above observed responses, we leveraged scRNA-seq datasets involving 16 kidney transplant biopsies ( 50 ) (Fig. 5H and fig.…”