Relating Molecular T Cell-mediated Rejection Activity in Kidney Transplant Biopsies to Time and to Histologic Tubulitis and Atrophy-fibrosis

Katelynn S Madill-Thomsen, Georg A Böhmig, Jonathan Bromberg, Gunilla Einecke, Farsad Eskandary, Gaurav Gupta, Marek Myslak, Ondrej Viklicky, Agnieszka Perkowska-Ptasinska, Kim Solez, Philip F Halloran, the INTERCOMEX Investigators, Katelynn S Madill-Thomsen, Georg A Böhmig, Jonathan Bromberg, Gunilla Einecke, Farsad Eskandary, Gaurav Gupta, Marek Myslak, Ondrej Viklicky, Agnieszka Perkowska-Ptasinska, Kim Solez, Philip F Halloran, the INTERCOMEX Investigators

Abstract

Background: We studied the variation in molecular T cell-mediated rejection (TCMR) activity in kidney transplant indication biopsies and its relationship with histologic lesions (particularly tubulitis and atrophy-fibrosis) and time posttransplant.

Methods: We examined 175 kidney transplant biopsies with molecular TCMR as defined by archetypal analysis in the INTERCOMEX study ( ClinicalTrials.gov #NCT01299168). TCMR activity was defined by a molecular classifier.

Results: Archetypal analysis identified 2 TCMR classes, TCMR1 and TCMR2: TCMR1 had higher TCMR activity and more antibody-mediated rejection ("mixed") activity and arteritis but little hyalinosis, whereas TCMR2 had less TCMR activity but more atrophy-fibrosis. TCMR1 and TCMR2 had similar levels of molecular injury and tubulitis. Both TCMR1 and TCMR2 biopsies were uncommon after 2 y posttransplant and were rare after 10 y, particularly TCMR1. Within late TCMR biopsies, TCMR classifier activity and activity molecules such as IFNG fell progressively with time, but tubulitis and molecular injury were sustained. Atrophy-fibrosis was increased in TCMR biopsies, even in the first year posttransplant, and rose with time posttransplant. TCMR1 and TCMR2 both reduced graft survival, but in random forests, the strongest determinant of survival after biopsies with TCMR was molecular injury, not TCMR activity.

Conclusions: TCMR varies in intensity but is always strongly related to molecular injury and atrophy-fibrosis, which ultimately explains its effect on survival. We hypothesize, based on the reciprocal relationship with hyalinosis, that the TCMR1-TCMR2 gradient reflects calcineurin inhibitor drug underexposure, whereas the time-dependent decline in TCMR activity and frequency after the first year reflects T-cell exhaustion.

Conflict of interest statement

P.F.H. holds shares in Transcriptome Sciences Inc (TSI), a University of Alberta research company dedicated to developing molecular diagnostics, and is supported in part by a licensing agreement between TSI and Thermo Fisher and by a research grant from Natera. P.F.H. is a consultant to Natera. The other authors declare no conflicts of interest.

Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc.

Figures

FIGURE 1.
FIGURE 1.
Research plan. AMR, antibody-mediated rejection; PCA, principal component analysis; TCMR, T cell–mediated rejection.
FIGURE 2.
FIGURE 2.
Visualizing TCMR1 and TCMR2 archetypal groups. The 1679 biopsies are shown distributed by their rejection classifiers scores in PCA and colored by their archetype assignment, with y-axis PC2 and x-axis (A) PC1, and (B) PC3. A, TCMR1 and TCMR2 show a gradient across PC1, and TCMR1 is lower than TCMR2 in PC2. B, PC3 separates AMR stages but does not separate TCMR1 and TCMR2. C, TCMR1 and TCMR2 biopsies distributed by their AMR activity (y-axis, AMRProb classifier scores) vs their TCMR activity (x-axis, TCMRProb classifier scores). AMR activity was correlated with TCMR activity (Spearman correlation coefficient = 0.35, P = 1.8E–6). The biopsies from DSA-positive patients are indicated. AMR, antibody-mediated rejection; AMRProb, AMR-probability classifier; EAMR, early-stage molecular AMR; FAMR, fully developed molecular AMR; LAMR, late-stage molecular AMR; NR, no rejection; PC1, principal component 1; PC2, principal component 2; PC3, principal component 3; PCA, principal component analysis; TCMR, T cell–mediated rejection; TCMRProb, TCMR-probability classifier.
FIGURE 3.
FIGURE 3.
Rolling averages for the relationships between time posttransplant and the TCMR molecular classes and features in 1679 biopsies. Rolling averages over time posttransplant (A) showing the proportion of biopsies assigned TCMR1 and TCMR2 archetypes and (B) showing the TCMR-related classifier scores. (C) IFNG expression in archetype clusters over time posttransplant (shown as a linear scale). EAMR, early-stage molecular AMR; FAMR, fully developed molecular AMR; LAMR, late-stage molecular AMR; NR, no rejection; TCMR, T cell–mediated rejection.
FIGURE 4.
FIGURE 4.
Relationships between time posttransplant and the moving average scores for molecular and histologic features of the biopsies. Two biopsies were missing date of transplant and were excluded from the time courses. (A) Molecular features and TCMR-associated gene expression within 175 TCMR biopsies. (B) Histologic lesions within 175 TCMR biopsies. (C) The probability of ci lesion scores >1 per archetype group over time posttransplant, as calculated in logistic regression. AMR, antibody-mediated rejection; pAMR, possible antibody-mediated rejection; TCMR, T cell–mediated rejection; pTCMR, possible T cell–mediated rejection.
FIGURE 5.
FIGURE 5.
Survival analysis during 3 y postbiopsy (days), with 1 random biopsy per patient. (A) Actuarial survival curves by archetype group. (B) Random forests showing the variable importance (including molecular and histologic features) in the prediction of 3 y postbiopsy graft survival. TCMR, T cell–mediated rejection.

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