Molecular Diversity of Clinically Stable Human Kidney Allografts

Abstract

IMPORTANCE Clinical decision and immunosuppression dosing in kidney transplantation rely on transplant biopsy tissue histology even though histology has low specificity, sensitivity, and reproducibility for rejection diagnosis. The inclusion of stable allografts in mechanistic and clinical studies is vital to provide a normal, noninjured comparative group for all interrogative studies on understanding allograft injury.OBJECTIVE To refine the definition of a stable allograft as one that is clinically, histologically, and molecularly quiescent using publicly available transcriptomics data. DESIGN, SETTING, AND PARTICIPANTSIn this prognostic study, the National Center for Biotechnology Information Gene Expression Omnibus was used to search for microarray gene expression data from kidney transplant tissues, resulting in 38 studies from January 1, 2017, to December 31, 2018. The diagnostic annotations included 510 acute rejection (AR) samples, 1154 histologically stable (hSTA) samples, and 609 normal samples. Raw fluorescence intensity data were downloaded and preprocessed followed by data set merging and batch correction. MAIN OUTCOMES AND MEASURESThe primary measure was area under the receiver operating characteristics curve from a set of feature selected genes and cell types for distinguishing AR from normal kidney tissue. RESULTSWithin the 28 data sets, the feature selection procedure identified a set of 6 genes (KLF4, CENPJ, KLF2, PPP1R15A, FOSB, TNFAIP3) (area under the curve [AUC], 0.98) and 5 immune cell types (CD4 + T-cell central memory [Tcm], CD4 + T-cell effector memory [Tem], CD8 + Tem, natural killer [NK]cells, and Type 1 T helper [T H 1] cells) (AUC, 0.92) that were combined into 1 composite Instability Score (InstaScore) (AUC, 0.99). The InstaScore was applied to the hSTA samples: 626 of 1154 (54%) were found to be immune quiescent and redefined as histologically and molecularly stable (hSTA/mSTA); 528 of 1154 (46%) were found to have molecular evidence of rejection (hSTA/mAR) and should not have been classified as stable allografts. The validation on an independent cohort of 6 months of protocol biopsy samples in December 2019 showed that hSTA/mAR samples had a significant change in graft function (r = 0.52, P < .001) and graft loss at 5-year follow-up (r = 0.17). A drop by 10 mL/min/1.73m 2 in estimated glomerular filtration rate was estimated as a threshold in allograft transitioning from hSTA/mSTA to hSTA/mAR. CONCLUSIONS AND RELEVANCEThe results of this prognostic study suggest that the InstaScore could provide an important adjunct for comprehensive and highly quantitative phenotyping of protocol kidney transplant biopsy samples and could be integrated into clinical care for accurate estimation of subsequent patient clinical outcomes.

Allorecognition and the spectrum of kidney transplant rejection

“…38 Despite the clear association between ABMR, TCMR, and specific transcripts, important discrepancies between molecular and histologic diagnoses were noted by the Edmonton group, 39,40 leading to the development of an automated molecular diagnostic platform (Molecular Microscope MMDx), 41 and the proposition of novel molecular rejection archetypes. 42 Likewise, other groups have reported molecular heterogeneity in biopsies with similar microscopic appearances, 17,[43][44][45] A recent unsupervised clustering analysis based on cellular deconvolution and gene networks revealed distinct molecular phenotypes that did not match with the histologic diagnoses of ABMR and TCMR. 44 This molecular heterogeneity suggests that different immune-related pathways can lead to similar spatial patterns of graft injury.…”

Through the Looking Glass: Unraveling the Stage-Shift of Acute Rejection in Renal Allografts

“…Alloimmune injury domain of Q-Scores in the range of 32-55: expose a state of alloimmunity flux as the graft switches from a state of allograft health to early alloimmune injury. This domain enriches for molecular allograft injury, where early rejection may not have histologically developed fully yet and could be missed by a biopsy [15]. (C).…”

“…We highlight in this study that the evaluation of the health of an allograft has to be able to involve accurate assessment of the state of immune quiescence (Q-Score < 32), where immunosuppression minimization could be supported, as well as understand the phase-shift of alloimmune injury through early stages of molecular and cellular rejection where histological injury and clinical graft dysfunction are still lagging indicators [15] (Q score 32-55). Uncovering this early phase-shift in acute rejection provides an unprecedented window to proactively tweak immunosuppression and reverse allograft injury, such that the Q-Score declines to the quiescence range of <32.…”

Integrated Analysis of Prognostic Genes Associated With Ischemia–Reperfusion Injury in Renal Transplantation

“…Among these genes, KLF2 , KLF4 , and KLF6 are highly conserved zinc finger transcription factors that regulate cell apoptosis, proliferation, differentiation, and migration. KLF2 and KLF4 are proved to be highly expressed in the endothelium during the episodes of IRI and responsible for disease progression ( 39 , 40 ), while KLF6 targeting improved IRI-induced AKI through effects on inflammation, apoptosis, and renal function ( 41 ). Combined with our results, those prognostic genes may control the progression of RIRI to adversely affect long-term outcomes of posttransplant patients and would be possibly utilized as effective targets, which was also applicable for other confirmed prognostic genes in the current study.…”