Rameters observed between `non-progressors’ and `progressors’ to CAD with IF/TA included graft function at 24 months post-KT and histological findings. Unique molecular signature associated to CNIT Microarray FCCP web analyses identified 382 probesets, corresponding to 340 unique genes, differentially expressed between CNIT and NA biopsies, 789 probesets (679 genes) between AR and NA samples, and 3,667 probesets (2,817 genes) between IF/TA and control samples, respectively (FDR5 ). (Figure 2A). A comparison of the three gene lists revealed overlap in a Venn diagram for the genes differentially expressed in each of the conditions (Figure 2B). However, unique genes were also identified. Specifically, 64.2 of the genes identified as significant in CNIT biopsies were also associated with those in kidney graft biopsies with AR and IF/TA. Interesting, 108 genes (134 probesets) uniquely differentially expressed between NA and CNIT were identified. From the analysis of these 108 genes, the top molecular and cellular functions related with macropinocytosis signaling (p = 2.8E-03), inhibition of matrix metalloproteases (p = 1.1E-02), and remodeling of epithelial adherences junctions (p = 3.2E-02). From the analysis of the top tox lists, purchase BAY1217389 persistent ischemia reperfusion injury (mouse), TFG signaling, and long-term renal injury anti-oxidative response panel (rat) were identified. Moreover, genes associated with renal damage (renal tubular injury (CLDN1, CP, BMP4), interstitial fibrosis of kidney (MMP14, WDC2), and proliferation of epithelial cell lines (MET, MMP7, PTP4A1, TRPC4, TTR) were recognized. To evaluate the specificity of the identified CNIT markers, a group of patients undergoing CNI sparing protocol was used. Differentially expressed genes related to renal necrosis/ death (FDR 5 ) were up-regulated in CNIT group when compared to the non-CNI group. Specifically, apoptosis of renal tubule (predicted positive activation, z-score=2.0) with upregulation of genes like PARP1, SMAD3, THBS1, LCN2, MYD88, among others, were upregulated in the CNIT. Apoptosis of proximal tubule cells and cell death of renal tubule were also up-regulated in the CNIT group. Also, genes associated with apoptosis of podocytes (CCN1, CDKN1A, CDKN1B, ILK, MAPK14, PP3CA, TGFB1, TP53) were over expressed in CNIT samples. Interaction Networks and Functional Analysis for genes differentially expressed in CNIT Significant probe sets identified between CNIT and NA are shown in the Supplemental Table 1. From the analysis of significant genes between CNIT vs. NA samples using IPA,Am J Transplant. Author manuscript; available in PMC 2015 May 01.Maluf et al.Pagethe top two molecular and cellular function categories were cellular growth and proliferation (p = 1.8E-15 to 3.3E-03) and cell death and survival (p = 2.4E-11 to 3.3E-03). The analysis of top canonical pathways showed integrin signaling (p = 8.5E-04) and inhibition of matrix metalloproteases (p = 2.3E-03) as the more relevant. After scoring the significant genes against lists of genes known to be involved in a particular type of toxicity, acute renal failure (rat) (p= 9.8E-09), renal necrosis/cell death (p=9.7E-07), and persistent renal ischemiareperfusion injury panels (mouse) (p= 6.8E-04) were identified. Genes associated with renal necrosis and cell death were recognized, including up-regulation of BIRC5, FAS, LCN2 (apoptosis of renal tubular epithelial cells), MCL1, PAK2, SOD2 (apoptosis of mesangial cells), HIF1A (apoptosis o.Rameters observed between `non-progressors’ and `progressors’ to CAD with IF/TA included graft function at 24 months post-KT and histological findings. Unique molecular signature associated to CNIT Microarray analyses identified 382 probesets, corresponding to 340 unique genes, differentially expressed between CNIT and NA biopsies, 789 probesets (679 genes) between AR and NA samples, and 3,667 probesets (2,817 genes) between IF/TA and control samples, respectively (FDR5 ). (Figure 2A). A comparison of the three gene lists revealed overlap in a Venn diagram for the genes differentially expressed in each of the conditions (Figure 2B). However, unique genes were also identified. Specifically, 64.2 of the genes identified as significant in CNIT biopsies were also associated with those in kidney graft biopsies with AR and IF/TA. Interesting, 108 genes (134 probesets) uniquely differentially expressed between NA and CNIT were identified. From the analysis of these 108 genes, the top molecular and cellular functions related with macropinocytosis signaling (p = 2.8E-03), inhibition of matrix metalloproteases (p = 1.1E-02), and remodeling of epithelial adherences junctions (p = 3.2E-02). From the analysis of the top tox lists, persistent ischemia reperfusion injury (mouse), TFG signaling, and long-term renal injury anti-oxidative response panel (rat) were identified. Moreover, genes associated with renal damage (renal tubular injury (CLDN1, CP, BMP4), interstitial fibrosis of kidney (MMP14, WDC2), and proliferation of epithelial cell lines (MET, MMP7, PTP4A1, TRPC4, TTR) were recognized. To evaluate the specificity of the identified CNIT markers, a group of patients undergoing CNI sparing protocol was used. Differentially expressed genes related to renal necrosis/ death (FDR 5 ) were up-regulated in CNIT group when compared to the non-CNI group. Specifically, apoptosis of renal tubule (predicted positive activation, z-score=2.0) with upregulation of genes like PARP1, SMAD3, THBS1, LCN2, MYD88, among others, were upregulated in the CNIT. Apoptosis of proximal tubule cells and cell death of renal tubule were also up-regulated in the CNIT group. Also, genes associated with apoptosis of podocytes (CCN1, CDKN1A, CDKN1B, ILK, MAPK14, PP3CA, TGFB1, TP53) were over expressed in CNIT samples. Interaction Networks and Functional Analysis for genes differentially expressed in CNIT Significant probe sets identified between CNIT and NA are shown in the Supplemental Table 1. From the analysis of significant genes between CNIT vs. NA samples using IPA,Am J Transplant. Author manuscript; available in PMC 2015 May 01.Maluf et al.Pagethe top two molecular and cellular function categories were cellular growth and proliferation (p = 1.8E-15 to 3.3E-03) and cell death and survival (p = 2.4E-11 to 3.3E-03). The analysis of top canonical pathways showed integrin signaling (p = 8.5E-04) and inhibition of matrix metalloproteases (p = 2.3E-03) as the more relevant. After scoring the significant genes against lists of genes known to be involved in a particular type of toxicity, acute renal failure (rat) (p= 9.8E-09), renal necrosis/cell death (p=9.7E-07), and persistent renal ischemiareperfusion injury panels (mouse) (p= 6.8E-04) were identified. Genes associated with renal necrosis and cell death were recognized, including up-regulation of BIRC5, FAS, LCN2 (apoptosis of renal tubular epithelial cells), MCL1, PAK2, SOD2 (apoptosis of mesangial cells), HIF1A (apoptosis o.