Gene expression profiling in the remnant kidney model of wild type and kinin B1 and B2 receptor knockout mice

Comprehensive analysis of diabetic nephropathy expression profile based on weighted gene co-expression network analysis algorithm

Background

Diabetic nephropathy (DN) is the major complication of diabetes mellitus, and leading cause of end-stage renal disease. The underlying molecular mechanism of DN is not yet completely clear. The aim of this study was to analyze a DN microarray dataset using weighted gene co-expression network analysis (WGCNA) algorithm for better understanding of DN pathogenesis and exploring key genes in the disease progression.

Methods

The identified differentially expressed genes (DEGs) in DN dataset GSE47183 were introduced to WGCNA algorithm to construct co-expression modules. STRING database was used for construction of Protein-protein interaction (PPI) networks of the genes in all modules and the hub genes were identified considering both the degree centrality in the PPI networks and the ranked lists of weighted networks. Gene ontology and Reactome pathway enrichment analyses were performed on each module to understand their involvement in the biological processes and pathways. Following validation of the hub genes in another DN dataset (GSE96804), their up-stream regulators, including microRNAs and transcription factors were predicted and a regulatory network comprising of all these molecules was constructed.

Results

After normalization and analysis of the dataset, 2475 significant DEGs were identified and clustered into six different co-expression modules by WGCNA algorithm. Then, DEGs of each module were subjected to functional enrichment analyses and PPI network constructions. Metabolic processes, cell cycle control, and apoptosis were among the top enriched terms. In the next step, 23 hub genes were identified among the modules in genes and five of them, including FN1, SLC2A2, FABP1, EHHADH and PIPOX were validated in another DN dataset. In the regulatory network, FN1 was the most affected hub gene and mir-27a and REAL were recognized as two main upstream-regulators of the hub genes.

Conclusions

The identified hub genes from the hearts of co-expression modules could widen our understanding of the DN development and might be of targets of future investigations, exploring their therapeutic potentials for treatment of this complicated disease.

Proteomic analysis of anti-angiogenic effects by conbercept in the mice with oxygen induced retinopathy

AIM

To analyze the retinal proteomes with and without conbercept treatments in mice with oxygen-induced retinopathy (OIR) and identify proteins involved in the molecular mechanisms mediated by conbercept.

METHODS

OIR was induced in fifty-six C57BL/6J mouse pups and randomly divided into four groups. Group 1: Normal17 (n=7), mice without OIR and treated with normal air. Group 2: OIR12/EXP1 (n=14), mice received 75% oxygen from postnatal day (P) 7 to 12. Group 3: OIR17/Control (n=14), mice received 75% oxygen from P7 to P12 and then normal air to P17. Group 4: Lang17/EXP2 (n=21), mice received 75% oxygen from P7 to P12 with intravitreal injection of 1 µL conbercept at the concentration of 10 mg/mL at P12, and then normal air from P12 to P17. Liquid Chromatography-Mass Spectrometry (LC-MS)/MS data were reviewed to find proteins that were up-regulated after the conbercept treatment. Gene ontology (GO) analysis was performed of conbercept-mediated changes in proteins involved in single-organism processes, biological regulation, cellular processes, immune responses, metabolic processes, locomotion and multiple-organism processes.

RESULTS

Conbercept induced a reversal of hypoxia-inducible factor 1 signaling pathway as revealed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and also induced down-regulation of proteins involved in blood coagulation and fibrin clot formation as demonstrated by the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the stimulation of interferon genes studies. These appear to be risk factors of retinal fibrosis. Additional conbercept-specific fibrosis risk factors were also identified and may serve as therapeutic targets for fibrosis.

CONCLUSION

Our studies reveal that many novel proteins are differentially regulated by conbercept. The new insights may warrant a valuable resource for conbercept treatment.

The polycomb proteins EZH1 and EZH2 co-regulate chromatin accessibility and nephron progenitor cell lifespan in mice

SIX2 (SIX homeobox 2)-positive nephron progenitor cells (NPCs) give rise to all epithelial cell types of the nephron, the filtering unit of the kidney. NPCs have a limited lifespan and are depleted near the time of birth. Epigenetic factors are implicated in the maintenance of organ-restricted progenitors such as NPCs, but the chromatin-based mechanisms are incompletely understood. Here, using a combination of gene targeting, chromatin profiling, and single-cell RNA analysis, we examined the role of the murine histone 3 Lys-27 (H3K27) methyltransferases EZH1 (enhancer of zeste 1) and EZH2 in NPC maintenance. We found that EZH2 expression correlates with NPC growth potential and that EZH2 is the dominant H3K27 methyltransferase in NPCs and epithelial descendants. Surprisingly, NPCs lacking H3K27 trimethylation maintained their progenitor state but cycled slowly, leading to a smaller NPC pool and formation of fewer nephrons. Unlike Ezh2 loss of function, dual inactivation of Ezh1 and Ezh2 triggered overexpression of the transcriptional repressor Hes-related family BHLH transcription factor with YRPW motif 1 (Hey1), down-regulation of Six2, and unscheduled activation of Wnt4-driven differentiation, resulting in early termination of nephrogenesis and severe renal dysgenesis. Double-mutant NPCs also overexpressed the SIX family member Six1 However, in this context, SIX1 failed to maintain NPC stemness. At the chromatin level, EZH1 and EZH2 restricted accessibility to AP-1-binding motifs, and their absence promoted a regulatory landscape akin to differentiated and nonlineage cells. We conclude that EZH2 is required for NPC renewal potential and that tempering of the differentiation program requires cooperation of both EZH1 and EZH2.

Histone deacetylases 1 and 2 regulate the transcriptional programs of nephron progenitors and renal vesicles

Nephron progenitor cells (NPCs) are Six2-positive metanephric mesenchyme cells, which undergo self-renewal and differentiation to give rise to nephrons until the end of nephrogenesis. Histone deacetylases (HDACs) are a group of epigenetic regulators that control cell fate, but their role in balancing NPC renewal and differentiation is unknown. Here, we report that NPC-specific deletion of Hdac1 and Hdac2 genes in mice results in early postnatal lethality owing to renal hypodysplasia and loss of NPCs. HDAC1/2 interact with the NPC renewal regulators Six2, Osr1 and Sall1, and are co-bound along with Six2 on the Six2 enhancer. Although the mutant NPCs differentiate into renal vesicles (RVs), Hdac1/2 mutant kidneys lack nascent nephrons or mature glomeruli, a phenocopy of Lhx1 mutants. Transcriptional profiling and network analysis identified disrupted expression of Lhx1 and its downstream genes, Dll1 and Hnf1a/4a, as key mediators of the renal phenotype. Finally, although HDAC1/2-deficient NPCs and RVs overexpress hyperacetylated p53, Trp53 deletion failed to rescue the renal dysgenesis. We conclude that the epigenetic regulators HDAC1 and HDAC2 control nephrogenesis via interactions with the transcriptional programs of nephron progenitors and renal vesicles.

Urinary Kininogen-1 and Retinol binding protein-4 respond to Acute Kidney Injury: predictors of patient prognosis?

Implementation of therapy for acute kidney injury (AKI) depends on successful prediction of individual patient prognosis. Clinical markers as serum creatinine (sCr) have limitations in sensitivity and early response. The aim of the study was to identify novel molecules in urine which show altered levels in response to AKI and investigate their value as predictors of recovery. Changes in the urinary proteome were here investigated in a cohort of 88 subjects (55 AKI patients and 33 healthy donors) grouped in discovery and validation independent cohorts. Patients’ urine was collected at three time points: within the first 48 h after diagnosis(T1), at 7 days of follow-up(T2) and at discharge of Nephrology(T3). Differential gel electrophoresis was performed and data were confirmed by Western blot (WB), liquid chromatography/mass spectrometry (LC-MS/MS) and enzyme-linked immunosorbent assay (ELISA). Retinol binding protein 4 (RBP4) and kininogen-1 (KNG1) were found significantly altered following AKI. RBP4 increased at T1, and progressively decreased towards normalization. Maintained decrease was observed for KNG1 from T1. Individual patient response along time revealed RBP4 responds to recovery earlier than sCr. In conclusion, KNG1 and RBP4 respond to AKI. By monitoring RBP4, patient’s recovery can be anticipated pointing to a role of RBP4 in prognosis evaluation.

Unmasking Silent Endothelial Activation in the Cardiovascular System Using Molecular Magnetic Resonance Imaging

Endothelial activation is a hallmark of cardiovascular diseases, acting either as a cause or a consequence of organ injury. To date, we lack suitable methods to measure endothelial activation in vivo. In the present study, we developed a magnetic resonance imaging (MRI) method allowing non-invasive endothelial activation mapping in the vasculature of the main organs affected during cardiovascular diseases. In clinically relevant contexts in mice (including systemic inflammation, acute and chronic kidney diseases, diabetes mellitus and normal aging), we provided evidence that this method allows detecting endothelial activation before any clinical manifestation of organ failure in the brain, kidney and heart with an exceptional sensitivity. In particular, we demonstrated that diabetes mellitus induces chronic endothelial cells activation in the kidney and heart. Moreover, aged mice presented activated endothelial cells in the kidneys and the cerebrovasculature. Interestingly, depending on the underlying condition, the temporospatial patterns of endothelial activation in the vascular beds of the cardiovascular system were different. These results demonstrate the feasibility of detecting silent endothelial activation occurring in conditions associated with high cardiovascular risk using molecular MRI.

Histone deacetylase 1 and 2 regulate Wnt and p53 pathways in the ureteric bud epithelium

Histone deacetylases (HDACs) regulate a broad range of biological processes through removal of acetyl groups from histones as well as non-histone proteins. Our previous studies showed that Hdac1 and Hdac2 are bound to promoters of key renal developmental regulators and that HDAC activity is required for embryonic kidney gene expression. However, the existence of many HDAC isoforms in embryonic kidneys raises questions concerning the possible specificity or redundancy of their functions. We report here that targeted deletion of both the Hdac1 and Hdac2 genes from the ureteric bud (UB) cell lineage of mice causes bilateral renal hypodysplasia. One copy of either Hdac1 or Hdac2 is sufficient to sustain normal renal development. In addition to defective cell proliferation and survival, genome-wide transcriptional profiling revealed that the canonical Wnt signaling pathway is specifically impaired in UB(Hdac1,2-/-) kidneys. Our results also demonstrate that loss of Hdac1 and Hdac2 in the UB epithelium leads to marked hyperacetylation of the tumor suppressor protein p53 on lysine 370, 379 and 383; these post-translational modifications are known to boost p53 stability and transcriptional activity. Genetic deletion of p53 partially rescues the development of UB(Hdac1,2-/-) kidneys. Together, these data indicate that Hdac1 and Hdac2 are crucial for kidney development. They perform redundant, yet essential, cell lineage-autonomous functions via p53-dependent and -independent pathways.

Global renal gene expression profiling analysis in B2-kinin receptor null mice: impact of diabetes

Diabetic nephropathy (DN), the leading cause of end-stage renal failure, is clinically manifested by albuminuria and a progressive decline in glomerular filtration rate. The risk factors and mechanisms that contribute to the development and progression of DN are still incompletely defined. To address the involvement of bradykinin B₂-receptors (B₂R) in DN, we used a genome wide approach to study the effects of diabetes on differential renal gene expression profile in wild type and B₂R knockout (B₂R^−/−) mice. Diabetes was induced with streptozotocin and plasma glucose levels and albumin excretion rate (AER) were measured at predetermined times throughout the 23 week study period. Longitudinal analysis of AER indicated that diabetic B₂R^−/−D null mice had a significantly decreased AER levels compared to wild type B₂R^+/+D mice (P = 0.0005). Results from the global microarray study comparing gene expression profiles among four groups of mice respectively: (B₂R^+/+C, B₂R^+/+D, B₂R^−/−C and B₂R^−/−D) highlighted the role of several altered pathological pathways in response to disruption of B₂R and to the diabetic state that included: endothelial injury, oxidative stress, insulin and lipid metabolism and inflammatory process with a marked alteration in the pro-apoptotic genes. The findings of the present study provide a global genomics view of biomarkers that highlight the mechanisms and putative pathways involved in DN.

Regulation of kidney development by histone deacetylases

There is accumulating evidence that gene expression can be regulated independently of DNA sequence changes, also called epigenetic modifications. Histone deacetylases (HDACs), a specific epigenetic group of enzymes, dynamically and reversibly removes acetyl groups from histone tails projecting from the nucleosome. Clinically, valproic acid fetopathy sheds some insight into the effects of altered HDACs on human embryonic development, since valproic acid is an antiepileptic drug and an HDAC inhibitor. The fetal anomalies include severe renal dysgenesis, supporting the role played by HDACs in human kidney development. Our recent studies have shown that HDACs regulate the transcriptional networks required for controlling the cell cycle, Wnt signaling, and the pathway upstream of the GDNF/RET signaling pathway in the developing kidney. Here, we describe novel HDAC target genes not previously implicated in renal development based on studies using genome-wide microarrays. These genes can be divided into transcription factors, modulators of matrix biology, chromatin remodelers, and DNA repair genes. We also report that HDACs are requisite for tissue-specific gene expression.

Histone deacetylase (HDAC) activity is critical for embryonic kidney gene expression, growth, and differentiation

Histone deacetylases (HDACs) regulate fundamental biological processes such as cellular proliferation, differentiation, and survival via genomic and nongenomic effects. This study examined the importance of HDAC activity in the regulation of gene expression and differentiation of the developing mouse kidney. Class I HDAC1-3 and class II HDAC4, -7, and -9 genes are developmentally regulated. Moreover, HDAC1-3 are highly expressed in nephron precursors. Short term treatment of cultured mouse embryonic kidneys with HDAC inhibitors (HDACi) induced global histone H3 and H4 hyperacetylation and H3K4 hypermethylation. However, genome-wide profiling revealed that the HDAC-regulated transcriptome is restricted and encompasses regulators of the cell cycle, Wnt/β-catenin, TGF-β/Smad, and PI3K-AKT pathways. Further analysis demonstrated that base-line expression of key developmental renal regulators, including Osr1, Eya1, Pax2/8, WT1, Gdnf, Wnt9b, Sfrp1/2, and Emx2, is dependent on intact HDAC activity. Treatment of cultured embryonic kidney cells with HDACi recapitulated these gene expression changes, and chromatin immunoprecipitation assays revealed that HDACi is associated with histone hyperacetylation of Pax2/Pax8, Gdnf, Sfrp1, and p21. Gene knockdown studies demonstrated that HDAC1 and HDAC2 play a redundant role in regulation of Pax2/8 and Sfrp1 but not Gdnf. Long term treatment of embryonic kidneys with HDACi impairs the ureteric bud branching morphogenesis program and provokes growth arrest and apoptosis. We conclude that HDAC activity is critical for normal embryonic kidney homeostasis, and we implicate class I HDACs in the regulation of early nephron gene expression, differentiation, and survival.

Renal fibrosis and proteomics: current knowledge and still key open questions for proteomic investigation

Renal tubulo-interstitial fibrosis is a non-specific process, representing the final common pathway for all kidney diseases, irrespective of their initial cause, histological injury, or etiology, leading to gradual expansion of the fibrotic mass which destroys the normal structure of the tissue and results in organ dysfunction and, ultimately, in end-stage organ failure. Proteomic studies of the fibrotic pathophysiological mechanisms have been performed in cell cultures, animal models and human tissues, addressing some of the key issues. This article will review proteomic contribution to the raising current knowledge on renal fibrosis biology and also mention seminal open questions to which proteomic techniques and proteomists could fruitfully contribute.

Understanding kidney disease: toward the integration of regulatory networks across species

Animal models have long been useful in investigating both normal and abnormal human physiology. Systems biology provides a relatively new set of approaches to identify similarities and differences between animal models and human beings that may lead to a more comprehensive understanding of human kidney pathophysiology. In this review, we briefly describe how genome-wide analyses of mouse models have helped elucidate features of human kidney diseases, discuss strategies to achieve effective network integration, and summarize currently available web-based tools that may facilitate integration of data across species. The rapid progress in systems biology and orthology, as well as the advent of web-based tools to facilitate these processes, now make it possible to take advantage of knowledge from distant animal species in targeted identification of regulatory networks that may have clinical relevance for human kidney diseases.

Therapeutic advantage of angiotensin-converting enzyme inhibitors in patients with proteinuric chronic kidney disease

Angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB) is recommended for the treatment of hypertension in patients with chronic kidney disease (CKD). The relation of ACEI to renal prognosis was investigated in CKD patients in a retrospective cohort study. The objectives were patients with nondiabetic CKD of stage 4 or below receiving monotherapy with calcium channel blocker (CCB), ACEI, or ARB, and combination therapy. For the endpoint of progression to CKD stage 5, Cox's proportional hazards analysis was conducted with explanatory variables of age, sex, baseline estimated GFR (eGFR), and proteinuria (UP) at the start of the observation period, and final blood pressure (BP) and UP at completion of the observation period. Analyzed patients comprised 131 males and 117 females, with mean age of 47.8 years. Patients were observed for 44.2 months, and the parameters of final SBP, DBP, eGFR, and UP were 127.6 +/- 6.9 mmHg, 77.8 +/- 5.8 mmHg, 38.1 +/- 10.6 ml/min/1.73 m(2), and 1.08 +/- 0.57 g/gCr, respectively, where 42 patients progressed to CKD stage 5. Drugs of CCB, ACEI, and ARB types were administered to 93, 85, and 127 patients, respectively. In the multivariate analysis, extracted common prognostic factors included the baseline eGFR and final UP, the odds ratio of which was 0.876 (every increase by 1 ml/min of eGFR) and 2.229 (every increase by 1 g of UP), respectively. Among drugs in use, ACEI was an independent prognostic factor, whose odds ratio was 0.147. The present study suggests that ACEI is a prognostic factor independent of hypotensive action and UP in CKD patients.

Ontogeny of bradykinin B1 receptors in the mouse kidney

Kinins are vasoactive peptides that stimulate two G-protein coupled bradykinin receptors (B1R and B2R). B2R-knockout mice are salt sensitive and develop renal dysgenesis and hypertension if salt stressed during embryogenesis. B1R-knockout mice, on the other hand, are protected from inflammation and fibrosis. This study examined the spatiotemporal expression of B1R during renal organogenesis. The segmental nephron identity of B1R immunoreactivity was determined by costaining with markers of the collecting duct (Dolichos biflorus), proximal tubule (Dolichos tetraglonus), and nephron progenitors (Pax2). At E14.5, the B1R was confined to few cells in the metanephric mesenchyme. Abundance of B1R increased progressively during development. On E17.5, B1R was enriched in differentiating proximal tubular cells and by postnatal day 1, B1R was clearly expressed on the luminal aspect of the proximal tubule. Quantitative real-time PCR revealed that the levels of B1R mRNA more than double during renal maturation. We conclude that 1) B1R expression correlates closely with nephron maturation; 2) lack of B1R in nephron progenitors suggests that B1R is unlikely to play a role in early nephrogenesis; and 3) enrichment of B1R in maturing proximal tubule suggests a potential role for this receptor in terminal differentiation of the proximal nephron.

Aberrant protein expression in plasma and kidney tissue during experimental obstructive nephropathy

Kidney failure is a major health problem worldwide. Patients with end-stage renal disease require intensive medical support by dialysis or kidney transplantation. Current methods for diagnosis of kidney disease are either invasive or insensitive, and renal function may decline by as much as 50% before it can be detected using current techniques. The goal of this study was, therefore, to identify biomarkers of kidney disease (associated with renal fibrosis) that can be used for the development of a non-invasive clinical test for early disease detection. We utilized two protein-profiling technologies (SELDI-TOF MS and 2-D) to screen the plasma and kidney proteome for aberrantly expressed proteins in an experimental mouse model of unilateral uretric obstruction, which mimics the pathology of human renal disease. Several differentially regulated proteins were detected at the plasma level of day-3-obstructed animals, which included serum amyloid A1, fibrinogen α, haptoglobin precursor protein, haptoglobin and major urinary proteins 11 and 8. Differentially expressed proteins detected at the tissue level included ras-like activator protein 2, haptoglobin precursor protein, malate dehydrogenase, α enolase and murine urinary protein (all p<0.05 versus controls). Immunohistochemistry was used to confirm the up-regulation of fibrinogen. Interestingly, these proteins are largely separated into four major classes: (i) acute-phase reactants (ii) cell-signaling molecules (iii) molecules involved in cell growth and metabolism and (iv) urinary proteins. These results provide new insights into the pathology of obstructive nephropathy and may facilitate the development of specific assay(s) to detect and monitor renal fibrosis.