*Purpose: Chronic renal allograft rejection often leads to irreversible damage, despite intensification of immunosuppression (ISN). T cell phenotypes in this clinical setting are not well described. Evaluating T cell function on a transcriptional level, through single cell RNA-seq, reveals unique T cell subsets, such as stemness (naïve, effector precursor), terminal effector, or exhaustion, in kidney transplant recipients with chronic rejection.

*Methods: Peripheral blood mononuclear cells (PBMC) and allograft biopsies from 3 recipients off ISN showing chronic cellular/antibody mediated rejection were analyzed and compared. Living CD45⁺ cells were isolated, followed by 10x Genomics scRNA-seq and bioinformatic analysis using R platform. Cell clustering by uniform manifold approximation and projection (UMAP) visualization (Figure 1), and feature plot visualization of individual gene expression of transcription factors, cytokines/effector molecules, and cell surface receptors were used (Figure 2).

*Results: The majority of CD4⁺ and CD8⁺ T cells in PBMC highly expressed T cell stemness associated genes (TCF7, LEF1, CCR7, SELL, CD127, BCL2, etc; data not shown). However, most CD8⁺ T cells infiltrated in chronically rejected allografts appeared to lose stemness, becoming TCF7^–GZMB^hi effector T cells or TCF7^–PDCD1^hiHAVCR2^hi exhausted T cells (Figure 2A). Only some allograft CD4⁺ T cells maintained TCF7^hi stemness (Figure 2B).

*Conclusions: Through scRNA-seq, we identified a phenotypic transition from stemness to terminal effector or exhaustion among CD8⁺ T cells in chronic allograft rejection. Similarly, CD4⁺ T cells appeared to lose stemness, suggesting a transition to an effector state. Further investigation into the regulatory processes of this dynamic cellular change is necessary to identify therapeutic targets that can prevent irreversible allograft damage in chronic kidney rejection.

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