F proximal tubule cells), MAPT, and RAD51, while downregulation was observed for CSF1, MAP2K6, NDUFAB1, SIRT4, and STRA6. Filtering analysis found three functions for renal tubule 1-Deoxynojirimycin side effects injury including proximal tubular toxicity (p =6.5E-06; up-regulated: BTG2, CLDN1, CP, JUNB, ST6GAL1; down-regulated: ACAA1, BMP4, HADH), damage of renal tubule (p = 7.7E-03; up-regulated: DICER1, LCN2; downregulated: CSF1); and injury of renal tubule (up-regulated: DICER1). Of particular interest was a gene expression pattern associated with connective tissue development and function (p= 1.3E-07 to 2.9E-03, including 36 genes). This molecular pattern included up-regulated genes (ACTB, CCNA2, FAS, LTF, MET, among others) involved in proliferation of fibroblasts. Moreover, when examining up-regulated genes independently from those downregulated, genes associated with IL8 signaling (p = 6.5E-4), ILK signaling (p = 6.5E-04), and integrin signaling (p = 2.52E-5) were identified. Evaluation of Upstream Regulators in CNIT IPA identified several upstream regulators for the differentially expressed genes (1,105 upstream regulators). After filtering the list using a significant z-score, 84 regulators showing activated predictive states and 18 inhibited predictive states were observed. The prediction algorithm identified 3 upstream regulators that were also part of the significant gene list (Vegf (z-score= 4.0), IL6 (z-score= 3.5), TNF (z-score= 4.5) and TGFB1 (z-score= 3.7). The network generated by Vegf identified as upstream regulator and their identified target genes is shown in Figure 2A. Interestingly, most of these genes were differentially expressed in our data set and following the predicted trend (up or down regulation). Upstream regulators in IF/TA An upstream regulator analysis in IF/TA samples to evaluate differences in activation pathways leading to injury between IF/TA and CNIT samples identified molecules including IL1B, IFNG, IL6, IL1RN, SOCS1, JAG2, among others. Only the top predicted molecules were graphed along with their identified targets in Supplemental Figure 1A. Also, a similar analysis to identify potential regulatory miRNAs was performed (Supplemental Figure 1B). CNIT contribution to IF/TA development The contribution of CNIT induced gene expression changes to the development of IF/TA was evaluated using two strategies. First, comparison analysis between CNIT toxicity to IF/TA diagnosed samples was performed. No statistical differences in plasma through levels of CNI were present between CNIT and IF/TA samples from transplant recipients at theAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptAm J Transplant. Author manuscript; available in PMC 2015 May 01.Maluf et al.Pagetime of biopsy collection (7.9?.0 vs. 6.6?.3 ng/mL, respectively (p=0.67)). This comparison yielded 1,697 significant probesets (1,402 genes) between CNIT and IF/TA samples (Figure 3). Top molecular and cellular functions associated with these genes were cellular function and maintenance (p=1.PepstatinMedChemExpress Pepstatin A 25E-37 to 4.53E-07) and cellular development (p=2.9E-55 to 3.3E-09). Immune cell trafficking (p=1.7E-34 to 3.8E-07), tissue development (p=1.2E-23), and humoral immune response (p=2.4E-15 to 3.3E-07) were the top physiological system development and function associated with these genes. Both conditions (CNIT and IF/TA) presented activation of growth factor signaling with IGF, TGF beta, reninangiotensin, and VEGF being the top identified in CNIT samples, while EGF and.F proximal tubule cells), MAPT, and RAD51, while downregulation was observed for CSF1, MAP2K6, NDUFAB1, SIRT4, and STRA6. Filtering analysis found three functions for renal tubule injury including proximal tubular toxicity (p =6.5E-06; up-regulated: BTG2, CLDN1, CP, JUNB, ST6GAL1; down-regulated: ACAA1, BMP4, HADH), damage of renal tubule (p = 7.7E-03; up-regulated: DICER1, LCN2; downregulated: CSF1); and injury of renal tubule (up-regulated: DICER1). Of particular interest was a gene expression pattern associated with connective tissue development and function (p= 1.3E-07 to 2.9E-03, including 36 genes). This molecular pattern included up-regulated genes (ACTB, CCNA2, FAS, LTF, MET, among others) involved in proliferation of fibroblasts. Moreover, when examining up-regulated genes independently from those downregulated, genes associated with IL8 signaling (p = 6.5E-4), ILK signaling (p = 6.5E-04), and integrin signaling (p = 2.52E-5) were identified. Evaluation of Upstream Regulators in CNIT IPA identified several upstream regulators for the differentially expressed genes (1,105 upstream regulators). After filtering the list using a significant z-score, 84 regulators showing activated predictive states and 18 inhibited predictive states were observed. The prediction algorithm identified 3 upstream regulators that were also part of the significant gene list (Vegf (z-score= 4.0), IL6 (z-score= 3.5), TNF (z-score= 4.5) and TGFB1 (z-score= 3.7). The network generated by Vegf identified as upstream regulator and their identified target genes is shown in Figure 2A. Interestingly, most of these genes were differentially expressed in our data set and following the predicted trend (up or down regulation). Upstream regulators in IF/TA An upstream regulator analysis in IF/TA samples to evaluate differences in activation pathways leading to injury between IF/TA and CNIT samples identified molecules including IL1B, IFNG, IL6, IL1RN, SOCS1, JAG2, among others. Only the top predicted molecules were graphed along with their identified targets in Supplemental Figure 1A. Also, a similar analysis to identify potential regulatory miRNAs was performed (Supplemental Figure 1B). CNIT contribution to IF/TA development The contribution of CNIT induced gene expression changes to the development of IF/TA was evaluated using two strategies. First, comparison analysis between CNIT toxicity to IF/TA diagnosed samples was performed. No statistical differences in plasma through levels of CNI were present between CNIT and IF/TA samples from transplant recipients at theAuthor Manuscript Author Manuscript Author Manuscript Author ManuscriptAm J Transplant. Author manuscript; available in PMC 2015 May 01.Maluf et al.Pagetime of biopsy collection (7.9?.0 vs. 6.6?.3 ng/mL, respectively (p=0.67)). This comparison yielded 1,697 significant probesets (1,402 genes) between CNIT and IF/TA samples (Figure 3). Top molecular and cellular functions associated with these genes were cellular function and maintenance (p=1.25E-37 to 4.53E-07) and cellular development (p=2.9E-55 to 3.3E-09). Immune cell trafficking (p=1.7E-34 to 3.8E-07), tissue development (p=1.2E-23), and humoral immune response (p=2.4E-15 to 3.3E-07) were the top physiological system development and function associated with these genes. Both conditions (CNIT and IF/TA) presented activation of growth factor signaling with IGF, TGF beta, reninangiotensin, and VEGF being the top identified in CNIT samples, while EGF and.