A pilot trial assessing urinary gene expression profiling with an mRNA array for diabetic nephropathy

The role of CDH2 and MCP-1 mRNAs of blood extracellular vesicles in predicting early-stage diabetic nephropathy

Background

Extracellular vesicles (EVs), including exosomes and microvesicles, are involved in intercellular communication by transferring biomolecules such as mRNA, which has been shown to be as essential biomarkers for many physiological and pathological conditions such as diabetic nephropathy (DN). This study aimed to investigate the expression of CDH1, CDH2, MCP-1, and PAI-1 mRNAs in blood EVs of DN patients and to determine their accuracy in predicting early-stage DN.

Methods

We recruited 196 participants, including 35 overt DN patients, 53 incipient DN patients, 62 diabetic patients (DM), and 46 healthy individuals. Quantification of the mRNA profile of blood EVs was performed using the qRT-PCR method. The diagnostic performance of mRNA was evaluated using receiver operating characteristic analysis.

Results

The mRNA expression of CDH2 and MCP-1 was downregulated in overt DN group (0.22-fold change and 0.15-fold change, respectively) and incipient DN group (0.60-fold change and 0.43-fold change, respectively) compared to DM group (1.72-fold change and 2.77-fold change, respectively), while PAI-1 mRNA expression decreased in incipient DN group (0.70-fold change) and DM group (0.58-fold change) compared to control. However, the expression level of CDH1 mRNA was not significantly different among the four groups (p = 0.408). Moreover, CDH2 and MCP-1 mRNAs inversely correlated with creatinine (r = -0.370 and r = -0.361, p<0.001) and Alb/Cr ratio (r = -0.355 and r = -0.297, p<0.001). 1/CDH2 mRNA also predicted overt DN with an accuracy of 0.75 (95%CI: 0.65–0.85) and incipient DN with an accuracy of 0.61 (95%CI: 0.50–0.71) while 1/MCP-1 mRNA had an accuracy of 0.66 (95%CI: 0.55–0.77) for overt DN prediction and an accuracy of 0.61 (95%CI: 0.51–0.71) for incipient DN prediction.

Conclusion

CDH2 and MCP-1 mRNAs expression in blood EVs was decreased with the development of DN, suggesting the renoprotective effect of these mRNAs in diabetic individuals. Moreover, their quantifications could serve as diagnostic biomarkers for early-stage DN.

Long non-coding RNA Dlx6os1 serves as a potential treatment target for diabetic nephropathy via regulation of apoptosis and inflammation

The present study investigated the effect of long non-coding RNA (lncRNA) Dlx6os1 silencing on cell proliferation, apoptosis and fibrosis, and further explored its influence on the mRNA expression profile in mouse mesangial cells (MMCs) of a diabetic nephropathy (DN) cellular model. A DN cellular model was constructed in SV40 MES13 MMCs under high glucose conditions (30 mmol/l glucose culture). lncRNA Dlx6os1 short hairpin (sh)RNA plasmids and negative control (NC) shRNA plasmids were transfected into the MMCs of the DN cellular model as the sh-lncRNA group and sh-NC group respectively. The mRNA expression profile was determined in the sh-lncRNA and sh-NC groups. Compared with the sh-NC group, the cell proliferation, mRNA and protein expression levels of proliferative markers (cyclin D1 and proliferating cell nuclear antigen) as well as fibrosis markers (fibronectin and collagen I) were suppressed, whereas cell apoptosis was promoted in the sh-lncRNA group. The mRNA expression profile identified 423 upregulated mRNAs and 438 downregulated mRNAs in the sh-lncRNA group compared with the sh-NC group. Additionally, Gene Ontology/Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that the differentially expressed mRNAs were enriched in apoptosis and inflammation-related pathways. Further gene-set enrichment analysis of apoptosis and inflammation revealed that lncRNA Dlx6os1 inhibition promoted apoptosis and suppressed inflammation in MMCs of the DN cellular model. In conclusion, lncRNA Dlx6os1 may serve as a potential treatment target for DN via regulation of multiple apoptosis- and inflammation-related pathways.

Decreased Expression of Urinary Mammalian Target of Rapamycin mRNA Is Related to Chronic Renal Fibrosis in IgAN

Background

Renal fibrosis is a common outcome of all pathological types of chronic kidney disease (CKD). However, the noninvasive detection of renal fibrosis remains a challenge.

Methods

We collected urine samples from 154 biopsy-proven IgA nephropathy (IgAN) patients and 61 healthy controls. The expression of mTOR was measured and the correlation with renal function parameter and pathological indicators. The receiver operating characteristic (ROC) curve for the diagnosis of IgAN and renal fibrosis was calculated.

Results

The urinary mammalian target of rapamycin (mTOR) expression was decreased in IgAN patients. The expression of mTOR was correlated with serum creatinine, blood urea nitrogen, estimated glomerular filtration rate, 24 h proteinuria, and cystatin C. Further, the urinary mTOR expression was significantly decreased in severe renal fibrosis patients compared with mild or moderate renal fibrosis patients. Urinary mTOR expression was correlated with score of tubulointerstitial fibrosis (TIF) and score of glomerular sclerosis. The ROC curve showed that mTOR can diagnose IgAN at a cut-off value of 0.930 with the sensitivity of 90.2% and specificity of 73.8% and renal fibrosis at a cut-off value of 0.301 with the sensitivity of 71.7% and specificity of 64.8%.

Conclusion

Urinary mTOR mRNA expression was a potential biomarker for diagnosis of IgAN and renal fibrosis in IgAN patients.

Bioinformatics-based discovery of the urinary BBOX1 mRNA as a potential biomarker of diabetic kidney disease

Background

Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease (ESKD) in the world. Emerging evidence has shown that urinary mRNAs may serve as early diagnostic and prognostic biomarkers of DKD. In this article, we aimed to first establish a novel bioinformatics-based methodology for analyzing the “urinary kidney-specific mRNAs” and verify their potential clinical utility in DKD.

Methods

To select candidate mRNAs, a total of 127 Affymetrix microarray datasets of diabetic kidney tissues and other tissues from humans were compiled and analyzed using an integrative bioinformatics approach. Then, the urinary expression of candidate mRNAs in stage 1 study (n = 82) was verified, and the one with best performance moved on to stage 2 study (n = 80) for validation. To avoid potential detection bias, a one-step Taqman PCR assay was developed for quantification of the interested mRNA in stage 2 study. Lastly, the in situ expression of the selected mRNA was further confirmed using fluorescent in situ hybridization (FISH) assay and bioinformatics analysis.

Results

Our bioinformatics analysis identified sixteen mRNAs as candidates, of which urinary BBOX1 (uBBOX1) levels were significantly upregulated in the urine of patients with DKD. The expression of uBBOX1 was also increased in normoalbuminuric diabetes subjects, while remained unchanged in patients with urinary tract infection or bladder cancer. Besides, uBBOX1 levels correlated with glycemic control, albuminuria and urinary tubular injury marker levels. Similar results were obtained in stage 2 study. FISH assay further demonstrated that BBOX1 mRNA was predominantly located in renal tubular epithelial cells, while its expression in podocytes and urothelium was weak. Further bioinformatics analysis also suggested that tubular BBOX1 mRNA expression was quite stable in various types of kidney diseases.

Conclusions

Our study provided a novel methodology to identify and analyze urinary kidney-specific mRNAs. uBBOX1 might serve as a promising biomarker of DKD. The performance of the selected urinary mRNAs in monitoring disease progression needs further validation.

Electronic supplementary material

The online version of this article (10.1186/s12967-019-1818-2) contains supplementary material, which is available to authorized users.

Urinary Biomarkers of Renal Fibrosis

Renal fibrosis is the common pathological pathway of progressive CKD. The commonly used biomarkers in clinical practice are not optimal to detect injury or predict prognosis. Therefore, it is crucial to develop novel biomarkers to allow prompt intervention. Urine serves as a valuable resource of biomarker discovery for kidney diseases. Owing to the rapid development of omics platforms and bioinformatics, research on novel urinary biomarkers for renal fibrosis has proliferated in recent years. In this chapter, we discuss the current status and provide basic knowledge in this field. We present novel promising biomarkers including tubular injury markers, proteins related to activated inflammation/fibrosis pathways, CKD273, transcriptomic biomarkers, as well as metabolomic biomarkers. Furthermore, considering the complex nature of the pathogenesis of renal fibrosis, we also highlight the combination of biomarkers to further improve the diagnostic and prognostic performance.

Exosomal proteomic analysis reveals changes in the urinary proteome of rats with unilateral ureteral obstruction

Congenital urinary tract obstruction (UTO) is a commonly noted disorder with the potential to cause permanent loss of renal function. Due to the possibility of spontaneous resolution, postnatal management strategies require lengthy and invasive surveillance methods to monitor the status of renal function and severity of obstruction. Here, a quantitative proteome analysis of urinary exosomes from weanling rats with surgically introduced UTO identifies a number of candidate biomarkers with the potential to improve diagnostic and prognostic methods for this disease. Using gel-assisted digestion coupled to liquid chromatography/tandem mass spectrometry (LC–MS/MS), 318 proteins were identified. Relative protein quantitation by spectral counting showed 190 proteins with significant changes in abundance due to either partial or complete obstruction. Numerous proteins identified here have been shown to be similarly altered in abundance in other renal diseases that cause tubule apoptosis and interstitial fibrosis. Extrapolating the role of the proteins showing quantifiable changes in abundance here from other forms of renal disease suggests they have potential for clinical applicability as biomarkers of congenital UTO. Included in the list of identified proteins are markers of apoptosis, oxidative stress, fibrosis, inflammation, and tubular cell damage, which are commonly associated with UTO. This study therefore provides a number of candidate biomarkers that, following validation in children experiencing UTO, have the potential to improve postnatal management of this disease.

Urinary Biomarkers for Chronic Kidney Disease with a Focus on Gene Transcript

Objective:

In the upcoming era of precision medicine, searching for the early, noninvasive biomarkers has been the cornerstone and major challenge in the management of chronic kidney disease (CKD). Urine contains rich biological information which could be the ideal source for noninvasive biomarkers of CKD. This review will discuss the recent advance in urinary biomarker.

Data Sources:

This review was based on data in articles published in the PubMed databases up to June 20, 2017, with the following keywords: “Chronic kidney disease”, “Biomarker”, and “Urine”.

Study Selection:

Original articles and important reviews on urinary biomarker were selected for this review.

Results:

Urinary biomarker studies of CKD mainly focused on urine sediment, supernatant, and urinary extracellular vesicles. The gene transcript (microRNA [miRNA], messenger RNA [mRNA]) biomarkers have been recently shown with diagnostic potential for CKD reflecting kidney function and histological change. However, challenges regarding technique and data analysis need to be resolved before translation to clinic.

Conclusions:

Different fractions of urine contain rich information for biomarker discovery, among which urine (extracellular vesicles) mRNA, miRNA, might represent promising biomarker for CKD.

Protein Array-Based Detection of Proteins in Kidney Tissues from Patients with Membranous Nephropathy

Membranous nephropathy (MN) is an autoimmune inflammatory disease in which proteins related with plenty of biological processes play an important role. However, the role of these proteins in the pathogenesis of MN is still unclear. This study aimed to screen differential proteins in kidney tissue samples from MN patients by using protein arrays and determine the pathways involved in the pathogenesis of MN. This study first tested a quantitative protein array (QAH-INF-3) and two semiquantitative protein arrays (L-493 and L-507) with normal renal tissue and identified L-493 as the most appropriate assay to compare protein levels between MN tissues and normal control tissues. The L-493 array identified 66 differentially expressed proteins (DEPs) that may be associated with MN. The gene oncology (GO) and protein-protein interaction (PPI) analyses revealed several processes potentially involved in MN, including extracellular matrix disassembly and organization, cell adhesion, cell-cell signaling, cellular protein metabolic process, and immune response (P < 0.05). We suggest that these different pathways work together via protein signaling and result in the pathogenesis and progression of MN.

Dietary Wolfberry Extract Modifies Oxidative Stress by Controlling the Expression of Inflammatory mRNAs in Overweight and Hypercholesterolemic Subjects: A Randomized, Double-Blind, Placebo-Controlled Trial

In the present study, we evaluated the antioxidative and anti-inflammatory effects of an aqueous extract of wolfberry fruit (WBE) in mild hypercholesterolemic and overweight subjects. This study was a double-blind randomized trial of two parallel groups of free-living subjects (n = 53). The participants consumed the contents of an 80 mL pouch containing 13.5 g WBE or placebo after one meal per day over an 8-week period. Following 8 weeks of WBE supplementation, we observed a slight but significant decrease in erythrocyte superoxide dismutase activity and an increase in catalase activity. Furthermore, to assess endogenous DNA damage in lymphocytes, the alkaline comet assay was performed, showing that the percentage of DNA in the tail was significantly decreased by 8-week WBE intake. Additionally, the proportion of significantly deregulated mRNAs related to oxidative or inflammatory stress was considerably higher in the WBE intake group. The present data indicate that WBE intake has antioxidative and anti-inflammatory effects in overweight and hypercholesterolemic subjects by modulating mRNA expression.

Elevated expression levels of serum insulin-like growth factor-1, tumor necrosis factor-α and vascular endothelial growth factor 165 might exacerbate type 2 diabetic nephropathy

AIMS/INTRODUCTION

The present study aimed to determine the associations between expressions of insulin-like growth factor-1 (IGF-1), tumor necrosis factor-α (TNF-α) and vascular endothelial growth factor 165 (VEGF₁₆₅ ) in serum, and occurrence and development of type 2 diabetic nephropathy (DN).

MATERIALS AND METHODS

A total of 108 patients diagnosed as DN were randomly selected, including 50 patients in the microalbuminuria group, 44 patients in the macroalbuminuria group and 14 patients in the renal insufficiency group. Meanwhile, 97 healthy people were collected as a normal control group. Urinary albumin (UALB) and urine creatinine (Cr) of all participants were measured for 24 h, with their ratio (UALB/Cr) being calculated. Enzyme-linked immunosorbent assay was used to detect the serum concentrations of IGF-1, TNF-α and VEGF₁₆₅ .

RESULTS

The expressions of serum IGF-1, TNF-α and VEGF₁₆₅ in the type 2 DN patients were significantly higher than those in the control group (all P < 0.05). The expressions of serum IGF-1, TNF-α and VEGF₁₆₅ in the type 2 DN patients were positively correlated with UALB/Cr (all P < 0.05). As type 2 DN worsened, the expressions of serum IGF-1, TNF-α and VEGF₁₆₅ increased, and type 2 DN severity had positive correlations with serum IGF-1, TNF-α and VEGF₁₆₅ concentrations (all P < 0.05). There was a positive association between IGF-1 and TNF-α, IGF-1 and VEGF₁₆₅ , and TNF-α and VEGF₁₆₅ (all P < 0.05). Logistic regression analysis showed that IGF-1 and VEGF₁₆₅ were associated with the progression of DN (both P < 0.05).

CONCLUSIONS

Elevated expression levels of serum IGF-1, TNF-α and VEGF₁₆₅ might exacerbate type 2 DN.

Interaction of atypical cadherin Fat1 with SoHo adaptor proteins CAP/ponsin and ArgBP2

Mammalian Fat1 is a giant atypical cadherin/tumor suppressor involved in the regulation of cellular orientation, migration, and growth. Fat1 is implicated in the development of the brain, eye, and kidney. Altered expression or mutations of FAT1 are also associated with cancer and facioscapulohumeral muscular dystrophy (FSHD). Yet, the mechanistic functions of this pathway remain incompletely understood. Here, we report the identification of Sorbin-homology (SoHo) proteins as novel interaction partners of Fat1 by virtue of a yeast-two-hybrid screen. SoHo proteins play diverse roles as adaptor proteins in cell signaling, cell adhesion and sarcomere architecture, including altered expression in cancer and FSHD. Specifically, we found SoHo proteins CAP/ponsin-1 and -2 (Sorbs1) and ArgBP2 (Sorbs2) to interact with the cytoplasmic domain of Fat1. We mapped the interaction to a prolin-rich classic type II PXXP motif within Fat1 and to the three Src-homology (SH3) domains within SoHo proteins using mutant expression in yeast, pulldown assays, and cell culture. Functionally, endogenous ponsin-2 expression of NRK-52E cells at cellular leading edges was lost upon knockdown of Fat1. In summary, our data point to an interaction of Fat1 with SoHo proteins that is able to recruit SoHo proteins to sites of Fat1 expression.

A Systems Biology Overview on Human Diabetic Nephropathy: From Genetic Susceptibility to Post-Transcriptional and Post-Translational Modifications

Diabetic nephropathy (DN), a microvascular complication occurring in approximately 20-40% of patients with type 2 diabetes mellitus (T2DM), is characterized by the progressive impairment of glomerular filtration and the development of Kimmelstiel-Wilson lesions leading to end-stage renal failure (ESRD). The causes and molecular mechanisms mediating the onset of T2DM chronic complications are yet sketchy and it is not clear why disease progression occurs only in some patients. We performed a systematic analysis of the most relevant studies investigating genetic susceptibility and specific transcriptomic, epigenetic, proteomic, and metabolomic patterns in order to summarize the most significant traits associated with the disease onset and progression. The picture that emerges is complex and fascinating as it includes the regulation/dysregulation of numerous biological processes, converging toward the activation of inflammatory processes, oxidative stress, remodeling of cellular function and morphology, and disturbance of metabolic pathways. The growing interest in the characterization of protein post-translational modifications and the importance of handling large datasets using a systems biology approach are also discussed.

Urinary vimentin mRNA as a potential novel biomarker of renal fibrosis

Renal fibrosis is a histological outcome of chronic kidney disease (CKD) progression. However, the noninvasive detection of renal fibrosis remains a challenge. Here we constructed a renal fibrosis target mRNA array and used it to detect urinary mRNAs of CKD patients for investigating potential noninvasive biomarkers of renal fibrosis. We collected urine samples from 39 biopsy-proven CKD patients and 11 healthy controls in the training set. Urinary mRNA profiles of 86 genes showed a total of 21 mRNAs that were differentially expressed between CKD patients and controls ( P < 0.05), and vimentin (VIM) mRNA demonstrated the highest change fold of 9.99 in CKD vs. controls with robust correlations with decline of renal function and severity of tubulointerstitial fibrosis. Additionally, VIM mRNA further differentiated patients with moderate-to-severe fibrosis from none-to-mild fibrosis group with an area of the curve of 0.796 ( P = 0.008). A verification of VIM mRNA in the urine of an additional 96 patients and 20 controls showed that VIM is not only well correlated with renal function parameters but also correlated with proteinuria and renal fibrosis scores. Multiple logistic regression and receiver-operating characteristics analysis further showed that urine VIM mRNA is the best predictive parameter of renal fibrosis compared with estimated glomerular filtration rate, serum creatinine, and blood urea nitrogen. In addition, there is no improved predictive performance for the composite biomarkers to predict renal fibrosis severity compared with a single gene of VIM. Overall, urinary VIM mRNA might serve as a novel independent noninvasive biomarker to monitor the progression of kidney fibrosis.

Inhibition of Thrombin-Activated Fibrinolysis Inhibitor Increases Survival in Experimental Kidney Fibrosis

Uncontrolled diabetes, inflammation, and hypertension are key contributors to progressive renal fibrosis and subsequent loss of renal function. Reduced fibrinolysis appears to be a feature of ESRD, but its contribution to the fibrotic program has not been extensively studied. Here, we show that in patients with CKD, the activity levels of serum thrombin-activated fibrinolysis inhibitor and plasmin strongly correlated with the degree of renal function impairment. We made similar observations in rats after subtotal nephrectomy and tested whether pharmacologic inhibition of thrombin-activated fibrinolysis inhibitor with UK-396082 could reduce renal fibrosis and improve renal function. Compared with untreated animals, UK-396082-treated animals had reduced glomerular and tubulointerstitial fibrosis after subtotal nephrectomy. Renal function, as measured by an increase in creatinine clearance, was maintained and the rate of increase in proteinuria was reduced in UK-396082-treated animals. Furthermore, cumulative survival improved from 16% to 80% with inhibition of thrombin-activated fibrinolysis inhibitor. Taken together, these data support the importance of the fibrinolytic axis in regulating renal fibrosis and point to a potentially important therapeutic role for suppression of thrombin-activated fibrinolysis inhibitor activity.

Hydroxycamptothecin-induced apoptotic gene expression profiling by PCR array in human Tenon's capsule fibroblasts

Studies have indicated that hydroxycamptothecin (HCPT) induces apoptosis of fibroblasts. In this study, we investigated the apoptotic gene expression profiling in HCPT-treated -human Tenon's capsule fibroblasts (HTCFs) and identify the most implicated gene in apoptotic signaling of HTCFs by HCPT. Method HTCFs were incubated with HCPT at 0, 0.25 and 4 mg/L for 24, 48 and 72 h, respectively. Anti-proliferative effects were measured by MTT assay. Apoptosis was determined using the Annexin V-FITC/PI apoptosis detection kit and apoptotic cells were identified by flow cytometry. A PCR array was employed to analyze the most implicated apoptotic genes during HCPT-induced apoptosis in HTCFs. Results from our studies showed that HCPT induced apoptosis in HTCFs in a concentration-and time-dependent manner. The apoptotic HTCFs was increased by 9.38% with a multiplicity at 4 mg/L HCPT. PCR array demonstrated remarkable changes in 88 apoptotic genes, including 9 up-regulated genes and 36 down-regulated genes. HCPT treatment induced the upregulation of CHOP and downregulation of XIAP in HTCFs. To conclude, our results support HCPT induced the apoptosis of HTCFs, involving the activation of mitochondrial and endoplasmic reticulum stresses as well as the downregulation expression of XIAP.

High-Throughput Proteomic Approaches to the Elucidation of Potential Biomarkers of Chronic Allograft Injury (CAI)

This review focuses on the role of OMICs technologies, concentrating in particular on proteomics, in biomarker discovery in chronic allograft injury (CAI). CAI is the second most prevalent cause of allograft dysfunction and loss in the first decade post-transplantation, after death with functioning graft (DWFG). The term CAI, sometimes referred to as chronic allograft nephropathy (CAN), describes the deterioration of renal allograft function and structure as a result of immunological processes (chronic antibody-mediated rejection), and other non-immunological factors such as calcineurin inhibitor (CNI) induced nephrotoxicity, hypertension and infection. Current methods for assessing allograft function are costly, insensitive and invasive; traditional kidney function measurements such as serum creatinine and glomerular filtration rate (GFR) display poor predictive abilities, while the current “gold-standard” involving histological diagnosis with a renal biopsy presents its own inherent risks to the overall health of the allograft. As early as two years post-transplantation, protocol biopsies have shown more than 50% of allograft recipients have mild CAN; ten years post-transplantation more than 50% of the allograft recipients have progressed to severe CAN which is associated with diminishing graft function. Thus, there is a growing medical requirement for minimally invasive biomarkers capable of identifying the early stages of the disease which would allow for timely intervention. Proteomics involves the study of the expression, localization, function and interaction of the proteome. Proteomic technologies may be powerful tools used to identify novel biomarkers which would predict CAI in susceptible individuals. In this paper we will review the use of proteomics in the elucidation of novel predictive biomarkers of CAI in clinical, animal and in vitro studies.

Strategic applications of gene expression: from drug discovery/development to bedside

Gene expression is useful for identifying the molecular signature of a disease and for correlating a pharmacodynamic marker with the dose-dependent cellular responses to exposure of a drug. Gene expression offers utility to guide drug discovery by illustrating engagement of the desired cellular pathways/networks, as well as avoidance of acting on the toxicological pathways. Successful employment of gene-expression signatures in the later stages of drug development depends on their linkage to clinically meaningful phenotypic characteristics and requires a biologically meaningful mechanism combined with a stringent statistical rigor. Much of the success in clinical drug development is hinged on predefining the signature genes for their fitness for purposes of application. Specific examples are highlighted to illustrate the breadth and depth of the potential utility of gene-expression signatures in drug discovery and clinical development to targeted therapeutics at the bedside.