Reprogramming of Energy Metabolism in Human PKD1 Polycystic Kidney Disease: A Systems Biology Analysis

Abstract

Multiple alterations of cellular metabolism have been documented in experimental studies of autosomal dominant polycystic kidney disease (ADPKD) and are thought to contribute to its pathogenesis. To elucidate the molecular pathways and transcriptional regulators associated with the metabolic changes of renal cysts in ADPKD, we compared global gene expression data from human PKD1 renal cysts, minimally cystic tissues (MCT) from the same patients, and healthy human kidney cortical tissue samples. We found gene expression profiles of PKD1 renal cysts were consistent with the Warburg effect with gene pathway changes favoring increased cellular glucose uptake and lactate production, instead of pyruvate oxidation. Additionally, mitochondrial energy metabolism was globally depressed, associated with downregulation of gene pathways related to fatty acid oxidation (FAO), branched-chain amino acid (BCAA) degradation, the Krebs cycle, and oxidative phosphorylation (OXPHOS) in renal cysts. Activation of mTORC1 and its two target proto-oncogenes, HIF-1α and MYC, was predicted to drive the expression of multiple genes involved in the observed metabolic reprogramming (e.g., GLUT3, HK1/HK2, ALDOA, ENO2, PKM, LDHA/LDHB, MCT4, PDHA1, PDK1/3, MPC1/2, CPT2, BCAT1, NAMPT); indeed, their predicted expression patterns were confirmed by our data. Conversely, we found AMPK inhibition was predicted in renal cysts. AMPK inhibition was associated with decreased expression of PGC-1α, a transcriptional coactivator for transcription factors PPARα, ERRα, and ERRγ, all of which play a critical role in regulating oxidative metabolism and mitochondrial biogenesis. These data provide a comprehensive map of metabolic pathway reprogramming in ADPKD and highlight nodes of regulation that may serve as targets for therapeutic intervention.

Keywords: ADPKD; global gene profiling; metabolic reprogramming; renal cysts.

Figure 1

Gene expression profiles of human PKD1 renal cysts are consistent with the Warburg effect and increased pentose phosphate pathway (PPP) flux. Schematic summary of the upregulation of glycolysis and PPP (left) and downregulation of gluconeogenesis (right) in PKD1 renal cysts. Upregulated genes are shown in red, and downregulated genes in blue, with mean expression fold changes in brackets. Genes that were not differentially expressed are shown in black. Arrows indicate irreversible enzymatic steps, and bi-directional arrows indicate interconverting reversible reactions determined by substrate concentration. Asterisk * denotes rate-limiting enzymes.

Figure 2

Metabolic reprogramming in human PKD1 renal cysts. Downregulation of the majority of genes in branched-chain amino acid degradation (a), fatty acid degradation (b), the Krebs cycle (c), and oxidative phosphorylation (d) suggests defective mitochondrial oxidative metabolism in PKD1 renal cysts. (e) Upregulation of NAMPT and downregulation of QPRT suggest renal cysts may favor the salvage over the de novo pathway to produce NAD+. All genes listed in the panels were differentially expressed between the cysts and MCT samples with an FDR ≤ 1%. In the heatmap, each column represents an individual sample, and each row represents the Z-score scaled gene expression levels across all samples; white is the mean Z-score (set to 0), red indicates greater than the mean, and blue less than the mean. Z-scores are computed for individual genes by subtracting the mean and then dividing by the standard deviation.

Figure 3

Rewiring of GSH metabolism in human PKD1 renal cysts. (a) Schematic summary of the downregulation of the γ-glutamyl cycle and upregulation of Na+-independent cystine/glutamate antiporter xCT (encoded by SLC7A11), which may serve as important sources for maintaining the cysteine pool in PKD1 renal cysts. NADPH may be resupplied by the reduction of NADP+ via the pentose phosphate pathway. Upregulated genes are shown in red, and downregulated genes in blue, with mean expression fold-changes in brackets. Genes that were not differentially expressed are shown in black. Asterisk * denotes the rate-limiting enzyme or substrate. (b) Gene expression profiling showing the differentially expressed genes involved in GSH metabolism in PKD1 renal cysts. In the heatmap, each column represents an individual sample, and each row represents the Z-score scaled gene expression levels across all samples; white is the mean Z-score (set to 0), red indicates greater than the mean and blue, less than the mean. Z-scores are computed for individual genes by subtracting the mean and then dividing by the standard deviation. Abbreviations: GSH (glutathione); AA (amino acid); Glu (glutamate); Cys (cysteine); Gly (glycine); Met (methionine); ROS (reactive oxygen species); MTs (methyltransferases); SAM (S-adenosylmethionine); SAH (S-adenosylhomocysteine); GSSG (glutathione disulfide); NAPDH (nicotinamide adenine dinucleotide phosphate, reduced); SOD (superoxide dismutase); CAT (catalase); GST (glutathione S-transferase); GPX (glutathione peroxidase); PRDX (peroxiredoxin).

Figure 4

Schematic summary of interrelationships between growth factors and energy sensing pathways in PKD1 renal cysts. Cysts switch from oxidative metabolism (fatty acid oxidation, branched-chain amino acid degradation, the Krebs cycle, oxidative phosphorylation, and peroxisomal proteins) to aerobic glycolysis to meet their energy needs. The PI3K/Akt pathway is activated upon growth factor/receptor tyrosine kinase stimulation (e.g., IGF1/IGF1R). The mTORC1 pathway integrates signals from growth factor stimulation, amino acid availability, and energy status via AMPK. The oncogenes HIF-1α and MYC together drive the expression of genes promoting aerobic glycolysis and the NAD+ salvage pathway. Upregulated pathways/genes are shown in red, and downregulated pathways/genes in blue, with mean expression fold-changes in brackets. Genes that were not differentially expressed are shown in black. Asterisk * denotes proteins that were predicted to be activated (red) or inhibited (blue) by GSEA or URA. Abbreviations: BCAA (branched-chain amino acid); BCKA (branched-chain α-keto acid); α-KG (α-ketoglutarate); OXPHOS (oxidative phosphorylation); Glu (glutamate); Gln (glutamine); NEAA (non-essential amino acids); ROS (reactive oxygen species); NAD (nicotinamide adenine dinucleotide); NAM (nicotinamide); NMN (nicotinamide mononucleotide).