Background: Ischemia reperfusion (I/R) injury affects early graft function and the recovery process that varies greatly among kidney transplant recipients. Involvement of both donor and recipient characteristics need to be considered to understand the mechanisms underlying early response to I/R injury. We thereby did an early longitudinal molecular analysis of pre-implant (K1) and post-reperfusion (K2) renal allograft biopsies and used novel techniques to understand the molecular mechanisms behind the I/R injury and recovery in this complex setting of transplantation.
Methods: A total of 146 early longitudinal biopsies collected from 73 kidney transplant recipients (KTRs) were used in this study. Gene expression (Affymetrix HG-U133Av2 Gene Chips) arrays were performed on all allograft biopsies. Gene expression analysis was done using expression and transcriptome console softwares. The similarity matrices between the paired repeat measure arrays, ie at the two different time points, were measured. Probe sets were considered significant when the false discovery rate (FDR) was < 5 % and fold change greater than 1.5.  Unsupervised principal component analysis (PCA) was done on all samples. Significantly differentially expressed probe sets were analyzed using IPA software.
Results: PCA of gene expression data from pre-implant biopsies showed 2 separate clusters (grp I; grp II). Two clusters were seen upon analyzing post-reperfusion biopsies as well. However, upon combining the longitudinal repeat measures from each sample, and studying the similarity matrices, 3 distinct groups were observed. The third cluster (grp IIb) consisted of samples that grouped with grp I at pre-implant stage and shifted to grp II at post-reperfusion stage. These biopsies had the maximum differentially expressed genes between K1 and K2 biopsies. Groups II and IIb were the high risk groups for DGF and also lower recovery at one month post-transplantation. A detailed analysis of the pathways involved in I/R injury in each of these groups showed clear differences in metabolic and inflammatory pathways. The high risk groups either had exacerbated inflammatory response involving cytokines like TNF-α, LIF and other inflammatory molecules like C5AR1 (Grp II), or showed inhibition of majority of the inflammatory pathways like inhibition of dendritic cell maturation, eNOS signaling with down regulation of genes like CD40, MHC II, CD1 (Grp IIb).
Conclusion: The analysis shows that balanced gene expression and regulation are key factors for immediate functioning and recovery of the kidney post I/R injury. The markers from each of these groups together with clinical data can determine efficiently high risk group for DGF and worse short term outcomes. Further analysis will help delineate necessary therapeutic intervention for recovery of kidney function post I/R injury after renal transplantation.