A Computational Gene Expression Score for Predicting Immune Injury in Renal Allografts

Abstract

Background: Whole genome microarray meta-analyses of 1030 kidney, heart, lung and liver allograft biopsies identified a common immune response module (CRM) of 11 genes that define acute rejection (AR) across different engrafted tissues. We evaluated if the CRM genes can provide a molecular microscope to quantify graft injury in acute rejection (AR) and predict risk of progressive interstitial fibrosis and tubular atrophy (IFTA) in histologically normal kidney biopsies.

Methods: Computational modeling was done on tissue qPCR based gene expression measurements for the 11 CRM genes in 146 independent renal allografts from 122 unique patients with AR (n = 54) and no-AR (n = 92). 24 demographically matched patients with no-AR had 6 and 24 month paired protocol biopsies; all had histologically normal 6 month biopsies, and 12 had evidence of progressive IFTA (pIFTA) on their 24 month biopsies. Results were correlated with demographic, clinical and pathology variables.

Results: The 11 gene qPCR based tissue CRM score (tCRM) was significantly increased in AR (5.68 ± 0.91) when compared to STA (1.29 ± 0.28; p < 0.001) and pIFTA (7.94 ± 2.278 versus 2.28 ± 0.66; p = 0.04), with greatest significance for CXCL9 and CXCL10 in AR (p <0.001) and CD6 (p<0.01), CXCL9 (p<0.05), and LCK (p<0.01) in pIFTA. tCRM was a significant independent correlate of biopsy confirmed AR (p < 0.001; AUC of 0.900; 95% CI = 0.705-903). Gene expression modeling of 6 month biopsies across 7/11 genes (CD6, INPP5D, ISG20, NKG7, PSMB9, RUNX3, and TAP1) significantly (p = 0.037) predicted the development of pIFTA at 24 months.

Conclusions: Genome-wide tissue gene expression data mining has supported the development of a tCRM-qPCR based assay for evaluating graft immune inflammation. The tCRM score quantifies injury in AR and stratifies patients at increased risk of future pIFTA prior to any perturbation of graft function or histology.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1. Gene expression of tCRM genes in AR.

[A] Intra-allograft gene expression for tCRM genes increased in AR when compared to stable with the most significant differences seen between CXCL10 and CXCL9 (p = 0.0001). [B] The tCRM score is significantly increased in AR when compared to Stable (p = 0.0000057). Although there is increased in pIFTA progressors at 6 months, this difference did not meet significance (p = 0.05) until 24 months (p = 0.03). A threshold tCRM score of 2.24 as determined by the discovery set. [C] The tCRM score significantly predicts rejection with an AUC of 0.900 (p = 0.001, 95% CI = 0.823–0.976) with 82.7% sensitivity and 82.5% specificity.

Fig 2. tCRM score correlates with AR lesions and chronic allograft nephropathy.

[A] The tCRM score positively correlates significantly (p = 0.001) with the degree of infiltrates found on biopsy for the t-score = 0.722 and [B] i score = 0.736. [C] A tCRM score across a subset of 7 of the 11 genes differentiated most samples with pIFTA or progressors (3.29 ± 0.93) from no-AR patients (1.2 ± 0.18; p = 0.037). Stable/non-progressors (NP) and AR were highly distinguishable (1.198±0.1801 versus 5.582±0.8651; p = 0.0063). pIFTA/Progressors and AR were not different with regards to their tCRM scores (p = 0.16).