Systems biology of autosomal dominant polycystic kidney disease (ADPKD): computational identification of gene expression pathways and integrated regulatory networks

Abstract

To elucidate the molecular pathways that modulate renal cyst growth in ADPKD, we performed global gene profiling on cysts of different size (<1 ml, n = 5; 10-20 ml, n = 5; >50 ml, n = 3) and minimally cystic tissue (MCT, n = 5) from five PKD1 human polycystic kidneys using Affymetrix HG-U133 Plus 2.0 arrays. We used gene set enrichment analysis to identify overrepresented signaling pathways and key transcription factors (TFs) between cysts and MCT. We found down-regulation of kidney epithelial restricted genes (e.g. nephron segment-specific markers and cilia-associated cystic genes such as HNF1B, PKHD1, IFT88 and CYS1) in the renal cysts. On the other hand, PKD1 cysts displayed a rich profile of gene sets associated with renal development, mitogen-mediated proliferation, cell cycle progression, epithelial-mesenchymal transition, hypoxia, aging and immune/inflammatory responses. Notably, our data suggest that up-regulation of Wnt/beta-catenin, pleiotropic growth factor/receptor tyrosine kinase (e.g. IGF/IGF1R, FGF/FGFR, EGF/EGFR, VEGF/VEGFR), G-protein-coupled receptor (e.g. PTGER2) signaling was associated with renal cystic growth. By integrating these pathways with a number of dysregulated networks of TFs (e.g. SRF, MYC, E2F1, CREB1, LEF1, TCF7, HNF1B/ HNF1A and HNF4A), our data suggest that epithelial dedifferentiation accompanied by aberrant activation and cross-talk of specific signaling pathways may be required for PKD1 cyst growth and disease progression. Pharmacological modulation of some of these signaling pathways may provide a potential therapeutic strategy for ADPKD.

c-Myc Signalling in the Genetic Mechanism of Polycystic Kidney Disease

“…The five SBT transgenic lines generated had no gross or microscopic renal abnormalities. These findings showed that the upregulation of c-Fos and TGFα in cells of human ADPKD cysts (69,70,83,84) are not necessarily causative. Moreover these studies indicated that the PKD phenotype in SBM mice depends on the specific functions inherent to c-Myc itself and not simply on a general mitogenic deregulation of the renal epithelial cells (4,82).…”

“…Studies from human ADPKD tissues pointed to one or several signaling pathways that converge on c-Myc as a key "cystogenic" factor. Consistent with c-Myc being a central node in ADPKD, renal cellular energetics in ADPKD and even in the autosomal recessive form of PKD, ARPKD rely on activation of the glutaminolytic and glycolytic pathways, known to be c-Myc molecular metabolic targets in cancer (70,76).…”

“…Quantification of c-Myc and N-Myc expression in renal tissues from ADPKD patients revealed that all human ADPKD kidney biopsies showed highly elevated c-Myc levels (up to 15-fold) whereas N-Myc expression is unaffected (68). Analysis from ADPKD kidney biopsies using microarrays confirmed increased c-Myc expression (69,70). Significantly, expression levels of c-Myc in fetal ADPKD kidneys were increased by approximately 40-fold, indicating that c-Myc is induced in both early and advanced stages of ADPKD.…”

“…Insights into possible human polycystin networks and downstream effector pathways were acquired from global and candidate approaches on human ADPKD kidneys and cell lines. These studies reported activation of developmental pathways including Wnt, Sonic Hedgehog, Notch, Hippo, bone morphogenic protein/transforming growth factor-β (BMP/TGFβ), ERK and transforming growth factor-α (TGFα) signaling (69,70,(73)(74)(75) that are known to regulate the c-Myc early growth response gene (6)(7)(8)(9). Studies from human ADPKD tissues pointed to one or several signaling pathways that converge on c-Myc as a key "cystogenic" factor.…”

Cyst formation following disruption of intracellular calcium signaling

“…Thus, the functional contribution of InsP3R in cyst development cannot be discounted in future studies, where InsP3R and the Pkd genes are selectively knocked down in the kidney. Indeed, the one human gene expression study on ADPKD (with Pkd1 mutations only) reveals an altered expression of InsP3R between cystic and renal-cell carcinoma tissue (65).…”