Franny Jongbloed

88 CHAPTER 4 with the response of the non-protective CHO-free diet, we repeated the meta-analysis with the three protective diets and the CHO-free diet into the approximation, thus not excluding the 3-day CHO-free diet. This meta-analysis yielded 640 DEPS. The majority of these DEPS in common showed a similar fold change and directionality among the three protective dietary interventions. A pathway analysis of these DEPS demonstrated regulation of nuclear receptor signaling as well as inhibition of cellular stress and injury and biosynthesis pathways amongst the top 10 overrepresented pathway categories (Table 2). Adding the 3-day 30% DR diet in the meta-analysis yielded 279 DEPS. No significant enriched pathways emerged. The 10 highest enriched pathways are depicted in Table S3. Table 2. Overview of the top 10 overrepresented canonical pathways in the meta-analysis ranked by their P- value Canonical Pathway Pathway Category P- value Genes Ratio Z-score LXR/RXR Activation Nuclear Receptor Signaling 7.24 E -09 16/121 (13.2%) +0.302 FXR/RXR Activation Nuclear Receptor Signaling 3.63 E -06 13/127 (10.2%) N/A LPS/IL-1 Mediated Inhibition of RXR Function Nuclear Receptor Signaling 2.24 E -05 16/219 (7.3%) -2.646 Superpathway of Cholesterol Biosynthesis Fatty Acids and Lipids Biosynthesis, Sterol Biosynthesis 2.40 E -05 6/28 (21.4%) N/A NRF2-mediated Oxidative Stress Response Cellular Stress and Injury 3.72 E -05 14/180 (7.8%) -1.000 Aryl Hydrocarbon Receptor Signaling Cell Cycle Regulation; Apoptosis; Xenobiotic Metabolism, Nuclear Receptor Signaling 5.13 E -05 12/140 (8.6%) +1.633 PXR/RXR Activation Nuclear Receptor Signaling 9.12 E -05 8/67 (11.9%) N/A Intrinsic Prothrombin Activation Pathway Cardiovascular Signaling; Cellular Stress and Injury 3.47 E -03 5/29 (17.2%) N/A Superpathway of Geranylgeranyldiphosphate Biosynthesis I Cofactors, Prosthetic Groups and Electron Carriers Biosynthesis 3.98 E -03 4/17 (23.5%) N/A Aldosterone Signaling in Epithelial Cells Cardiovascular Signaling; Nuclear Receptor Signaling 4.57 E -03 11/152 (7.2%) N/A The top 10 overrepresented pathways derived from the 640 DEPS in common between 3-days of fasting, two weeks 30% DR, three days of a protein-free diet and three days of a carbohydrate-free diet. These pathways are mostly involved in regulation of nuclear receptor signalling (five out of 10), biosynthesis signalling (two out of 10) and cellular stress and injury (two out of 10). To further explore the regulated DEPS and pathways in relation to the protective response against renal IRI, we examined the involvement of upstream transcription factors (TFs) in the DEPS that emerged from the meta-analysis. In the meta-analysis, 16 TFs were identified of which 12 were predicted to be activated and six inhibited (Table 3). Critical