Perturbations of the T-cell immune repertoire in kidney transplant rejection

Abstract

In this cross-sectional and longitudinal analysis of mapping the T-cell repertoire in kidney transplant recipients, we have investigated and validated T-cell clonality, immune repertoire chronology at rejection, and contemporaneous allograft biopsy quantitative tissue injury, to better understand the pathobiology of acute T-cell fraction, T-cell repertoire and antibody-mediated kidney transplant rejection. To follow the dynamic evolution of T-cell repertoire changes before and after engraftment and during biopsy-confirmed acute rejection, we sequenced 323 peripheral blood samples from 200 unique kidney transplant recipients, with (n=100) and without (n=100) biopsy-confirmed acute rejection. We report that patients who develop acute allograft rejection, have lower (p=0.01) T-cell fraction even before transplantation, followed by its rise after transplantation and at the time of acute rejection accompanied by high TCR repertoire turnover (p=0.004). Acute rejection episodes occurring after the first 6 months post-transplantation, and those with a component of antibody-mediated rejection, had the highest turnover; p=0.0016) of their T-cell repertoire. In conclusion, we validated that detecting repertoire changes in kidney transplantation correlates with post-transplant rejection episodes suggesting that T-cell receptor sequencing may provide recipient pre-transplant and post-transplant predictors of rejection risk.

Keywords: T cell-mediated rejection; TCR sequencing; acute rejection; antibody-mediated rejection; immune repertoire; kidney transplantation.

Figure 1

Study schematics. Validation of repertoire turnover and T cell fraction on post-transplant paired samples with and without acute rejection. Ninety-two AR samples and 98 STA transplant samples passed QC (>500 T cells) with sufficient T cell-derived DNA yield for analysis.

Figure 2

Baseline characteristics of TCR clonality and T cell fraction at baseline for transplant recipients who have future rejection and no rejection. (A) There was a trend towards higher clonality in stable subjects, which could indicate a more diverse repertoire at baseline in subjects who will experience acute rejection. (B) There was no difference in baseline repertoire clonality between the groups with or without CMV positivity. (C) When assessed the baseline T cell fraction in stable compared to acute rejection subjects, subjects with lower T cell fractions at baseline are at increased risk of rejection (p=0.01). (D) When we analyzed for T-cell fraction among clean TCMR and ABMR cases, we observed a significant difference between the two types of rejection cohorts (Kruskal Wallis p=4.03e-06) with a lower value in ABMR relative to TCMR using a post-hoc Dunn test p=3.35e-6.

Figure 3

Significant increase in T-cell fraction at late rejection and in ABMR. (A) Increase of T-cell fraction is significant in late rejection cases >6 mo post-transplantation. (B) There is increase in T-cell fraction in ABMR compared to non-ABMR samples. (C) There was an increased peripheral T-cell fraction among AR subjects compared to STA among AR samples collected at 6 mo post-tx.

Figure 4

Morisita Index which measures similarity based on the number of shared sequences between two populations as well as how well represented those overlapping sequences are within the two populations was low in AR and in antibody mediated rejection. (A) The T cell repertoire turnover is higher (with low Morisita Index) in patients with AR at > 6 mo post transplantation. (B) The turnover of TCR was more pronounced in ABMR compared with patients with STA and TCMR. (C) There was a greater repertoire turnover at AR event compared to STA at matching post-tx timepoint at 6 mo.

Figure 5

The Morisita Index inversely proportional to microcirculation inflammation. The finding of increased TCR turnover in terms of low Morisita Index among AR (ABMR, TCMR, Mixed AR) patients was further demonstrated by a significant correlation.