Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease

Because of its availability, ease of collection, and correlation with physiology and pathology, urine is an attractive source for clinical proteomics/peptidomics. However, the lack of comparable data sets from large cohorts has greatly hindered the development of clinical proteomics. Here, we report the establishment of a reproducible, high resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins, ranging from 800 to 17,000 Da, using samples from 3,600 individuals analyzed by capillary electrophoresis coupled to MS. All processed data were deposited in an Structured Query Language (SQL) database. This database currently contains 5,010 relevant unique urinary peptides that serve as a pool of potential classifiers for diagnosis and monitoring of various diseases. As an example, by using this source of information, we were able to define urinary peptide biomarkers for chronic kidney diseases, allowing diagnosis of these diseases with high accuracy. Application of the chronic kidney disease-specific biomarker set to an independent test cohort in the subsequent replication phase resulted in 85.5% sensitivity and 100% specificity. These results indicate the potential usefulness of capillary electrophoresis coupled to MS for clinical applications in the analysis of naturally occurring urinary peptides.Chronic kidney disease (CKD)1 is often characterized by a slow, progressive loss of renal function with a loss of glomerular filtration over a period of months or years that may eventually lead to end stage renal disease (ESRD). Patients with ESRD require renal replacement therapy (dialysis or kidney transplantation). The most common causes of CKD in North America, Europe, and Japan are diabetic nephropathy, hypertension, and glomerulonephritis (1). Together, these diseases account for ∼75% of all adult cases of ESRD. Historically, kidney diseases were classified according to the anatomical compartment of the kidney that is involved. On this basis, vascular diseases include large and small vessel diseases, such as hypertensive nephropathy and vasculitis. Glomerular diseases comprise a diverse group of histologically defined primary glomerulopathies (e.g. focal segmental glomerulosclerosis (FSGS), membranous glomerulonephritis (MGN), minimal change disease (MCD), and IgA nephropathy (IgAN)) and secondary glomerulopathies due to diabetes mellitus (diabetic nephropathy), systemic autoimmune disorders (e.g. lupus erythematosus and hemolytic-uremic syndrome), or chronic viral infection (e.g. hepatitis and HIV). Tubular diseases are characterized by low molecular weight proteinuria and multiple transport defects (e.g. DeToni-Debré-Fanconi syndrome).In clinical practice, renal damage is generally detected by proteinuria/albuminuria on urinalysis or quantitative measurement, changes in serum creatinine concentration for estimation of glomerular filtration rate, or both. However, these methods have major limitations as they are nonspecific and frequently are also late manifestations of renal damage. Therefore, we have sought to define alternative biomarkers for renal damage that may enable earlier and more accurate disease assessment.Analysis of urine plays a central role in clinical diagnostics as it can be collected non-invasively. Urine as a body fluid for clinical analysis is relatively stable, probably due to the fact that it is “stored” for hours in the bladder; hence, proteolytic degradation by endogenous proteases may be essentially complete by the time of voiding (2). This is in sharp contrast to blood for which the activation of proteases and, consequently, generation of an array of proteolytic breakdown products are inevitably associated with its collection (3). The human urinary peptidome has been extensively investigated to gain insight about disease processes affecting the kidney and the urogenital tract (4–6). Urinary proteins and peptides originate not only from glomerular filtration but also from tubular secretion, epithelial cells shed from the kidney and urinary tract, secreted exosomes, and seminal secretions (7–9). Urine is a rich source of biomarkers for a wide range of diseases due to specific changes in its proteome (10–13). To test the feasibility of urinary proteomics as a non-invasive diagnostic tool, large scale studies are needed to analyze urine samples with reliable and quantitative experimental procedures. Various techniques have been applied to this effort, including two-dimensional electrophoresis combined with mass spectrometry (MS) and/or immunochemical identification of proteins (14–16), liquid chromatography coupled to mass spectrometry (LC-MS) (17, 18), and surface-enhanced laser desorption/ionization mass spectrometry (SELDI-MS) (19).Because of mostly technical challenges, studies relying on proteomics experimental procedures are often restricted to the comparison of two groups of subjects (i.e. healthy controls versus patients with a well defined disease entity) with only a few individuals in each group. The lack of comparability severely limits the suitability of such data for a meta-analysis approach to define broadly applicable biomarkers. Consequently, findings from several studies cannot be used to explore the human urinary proteome/peptidome in its entirety. In addition, the health state of patients with kidney disease is often too heterogeneous to be reliably classified by biomarkers identified by such a strictly single disease-oriented approach. Diagnosis of individuals with different stages or types of kidney disease (disease controls) is conceivable by multiplex screening of proteomics data. Realization of such an approach critically depends on the use of a measurement platform allowing analysis of proteomic profiles within a reasonably short time and with high resolution and on the generation of a reference database for the human urinary proteome/peptidome.Capillary electrophoresis coupled to mass spectrometry (CE-MS) enables reproducible and robust high resolution analysis of several thousand low molecular weight urinary proteins/peptides in less than an hour (5). In comparison with other proteomics methods, CE-MS offers several advantages. (i) It provides fast separation with high resolution. (ii) It is robust: capillaries are inexpensive and can be reconditioned efficiently using NaOH. (iii) It is compatible with most volatile buffers and analytes generally required for ESI. (iv) It provides a stable constant flow, avoiding the necessity of buffer gradients (for more details, see recent reviews (3, 5, 20)).This approach has recently been used to analyze urine samples from healthy individuals and patients with various chronic kidney diseases in several independent masked studies (21–27), including IgAN (28), diabetic nephropathy (29), and ANCA-associated vasculitis (30). The high number of data sets analyzed under identical conditions using the same technological platform allows comprehensive characterization of the low molecular weight proteome (peptidome) that can then become a primary source of information for the diagnosis, classification, and monitoring of a wide range of diseases. Here, we report the analysis of the human urinary peptidome by CE-MS and the identification of peptide urinary biomarkers for the detection of pathological changes in the kidney during the development of many forms of CKD. Furthermore, we have replicated these findings in an independent cohort.     

Naturally Occurring Mutations Alter the Stability of Polycystin-1 Polycystic Kidney Disease (PKD) Domains

Mutations in polycystin-1 (PC1) can cause autosomal dominant polycystic kidney disease, which is a leading cause of renal failure. The available evidence suggests that PC1 acts as a mechanosensor, receiving signals from the primary cilia, neighboring cells, and extracellular matrix. PC1 is a large membrane protein that has a long N-terminal extracellular region (about 3000 amino acids) with a multimodular structure including 16 Ig-like polycystic kidney disease (PKD) domains, which are targeted by many naturally occurring missense mutations. Nothing is known about the effects of these mutations on the biophysical properties of PKD domains. Here we investigate the effects of several naturally occurring mutations on the mechanical stability of the first PKD domain of human PC1 (HuPKDd1). We found that several missense mutations alter the mechanical unfolding pathways of HuPKDd1, resulting in distinct mechanical phenotypes. Moreover, we found that these mutations also alter the thermodynamic stability of a structurally homologous archaeal PKD domain. Based on these findings, we hypothesize that missense mutations may cause autosomal dominant polycystic kidney disease by altering the stability of the PC1 ectodomain, thereby perturbing its ability to sense mechanical signals.     

不同血液净化方式对慢性肾脏病矿物质和骨异常的疗效观察

目的:探讨2种不同血液净化方式对慢性肾脏病(CKD)患者低血钙、高血磷及高血清甲状旁腺激素的改善效果。方法:选择2011年9月到2014年9月在我院接收维持性血液透析(MHD)的患者64例,随机分为HDF组和HP-HD组各32例;HDF组采用血液透析滤过(HDF)治疗,HP-HD组采用血液灌流(HP)联合血液透析(HD)治疗;分别在治疗前及治疗后3周采血检测血钙、血磷和全段甲状旁腺激素(iPTH)。结果:治疗三周后,与治疗前相比较,两组患者血磷、iPTH显著下降,血钙显著上升,均有显著性差异(P0.05);HP-HD组患者血磷、iPTH下降较HDF组更为显著,均有显著性差异(P0.05)。结论:HDF和HP联合HD均能有效调节血钙、清除血磷和iPTH水平,但HP联合HD较HDF效果更佳。     

Ameliorative Effect of Chrysin on Adenine-Induced Chronic Kidney Disease in Rats

Chrysin (5, 7- dihydroxyflavone) is a flavonoid with several pharmacological properties that include antioxidant, anti-inflammatory and antiapoptotic activities. in this work, we investigated some effects of three graded oral doses of chrysin (10, 50 and 250 mg/kg) on kidney structure and function in rats with experimental chronic renal disease (CKD) induced by adenine (0.25% w/w in feed for 35 days), which is known to involve inflammation and oxidative stress. Using several indices in plasma, urine and kidney homogenates, adenine was found to impair kidney function as it lowered creatinine clearance and increased plasma concentrations of creatinine, urea, neutrophil gelatinase-associated lipocalin and N-Acetyl-beta-D-glucosaminidase activity. Furthermore, it raised plasma concentrations of the uremic toxin indoxyl sulfate, some inflammatory cytokines and urinary albumin concentration. Renal morphology was severely damaged and histopathological markers of inflammation and fibrosis were especially increased. In renal homogenates, antioxidant indices, including superoxide dismutase and catalase activities, total antioxidant capacity and reduced glutathione were all adversely affected. Most of these adenine – induced actions were moderately and dose -dependently mitigated by chrysin, especially at the highest dose. Chrysin did not cause any overt adverse effect on the treated rats. The results suggest that different doses of chrysin produce variable salutary effects against adenine-induced CKD in rats, and that, pending further pharmacological and toxicological studies, its usability as a possible ameliorative agent in human CKD should be considered.     

Effects of Naturally Occurring Six- and Twelve-Nucleotide Inserts on Newcastle Disease Virus Replication and Pathogenesis

Newcastle disease virus (NDV) isolates contain genomes of 15,186, 15,192 or 15,198 nucleotides (nt). The length differences reflect a 6-nt insert in the 5′ (downstream) non-translated region (NTR) of the N gene (15,192-nt genome) or a 12-nt insert in the ORF encoding the P and V proteins (causing a 4-amino acid insert; 15,198-nt genome). We evaluated the role of these inserts in the N and P genes on viral replication and pathogenicity by inserting them into genomes of two NDV strains that have natural genome lengths of 15,186 nt and represent two different pathotypes, namely the mesogenic strain Beaudette C (BC) and the velogenic strain GB Texas (GBT). Our results showed that the 6-nt and 12-nt inserts did not detectably affect N gene expression or P protein function. The inserts had no effect on the replication or virulence of the highly virulent GBT strain but showed modest degree of attenuation in mesogenic strain BC. We also deleted a naturally-occurring 6-nt insertion in the N gene from a highly virulent 15,192-nt genome-length virus, strain Banjarmasin. This resulted in reduced replication in vitro and reduced virulence in vivo. Thus, although these inserts had no evident effect on gene expression, protein function, or replication in vivo, they did affect virulence in two of the three tested strains.     

Circulating Adipocytokines and Chronic Kidney Disease

Background

Adipokines have been associated with atherosclerotic heart disease, which shares many common risk factors with chronic kidney disease (CKD), but their relationship with CKD has not been well characterized.

Methods

We investigated the association of plasma leptin, resistin and adiponectin with CKD in 201 patients with CKD and 201 controls without. CKD was defined as estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m² or presence of albuminuria. Quantile regression and logistic regression models were used to examine the association between adipokines and CKD adjusting for multiple confounding factors.

Results

Compared to controls, adjusted median leptin (38.2 vs. 17.2 ng/mL, p<0.0001) and adjusted mean resistin (16.2 vs 9.0 ng/mL, p<0.0001) were significantly higher in CKD cases. The multiple-adjusted odds ratio (95% confidence interval) of CKD comparing the highest tertile to the lower two tertiles was 2.3 (1.1, 4.9) for leptin and 12.7 (6.5, 24.6) for resistin. Median adiponectin was not significantly different in cases and controls, but the odds ratio comparing the highest tertile to the lower two tertiles was significant (1.9; 95% CI, 1.1, 3.6). In addition, higher leptin, resistin, and adiponectin were independently associated with lower eGFR and higher urinary albumin levels.

Conclusions

These findings suggest that adipocytokines are independently and significantly associated with the risk and severity of CKD. Longitudinal studies are warranted to evaluate the prospective relationship of adipocytokines to the development and progression of CKD.     

Effect of Naturally Occurring nif Reiterations on Symbiotic Effectiveness in Rhizobium phaseoli

Most naturally occurring strains of Rhizobium phaseoli possess reiteration of the nif genes. Three regions contain nitrogenase structural genes in strain CFN42. Two of these regions (a and b) have copies of nifH, nifD, and nifK, whereas the third region (c) contains only nifH. Strains containing mutations in either nif region a or nif region b had significantly diminished symbiotic effectiveness compared with the wild-type strain on the basis of nodule mass, total nitrogenase activity per plant, nitrogenase specific activity, total nitrogen in the shoot, and percentage of nitrogen. A strain containing mutations in both nif region a and nif region b was totally ineffective. These data indicate that both nif region a and nif region b are needed for full symbiotic effectiveness in R. phaseoli.     

Relationship Between Hyperuricemia and Chronic Kidney Disease

Because approximately 70% of uric acid is excreted from the kidney, hyperuricemia occurs when renal function deteriorates. Until now, it has not been clear if the hyperuricemia seen in such renal diseases plays a role in the progression of renal disease. However, recent clinical studies show that the serum uric acid value is closely associated with hypertension in hyperuricemic patients (cross-sectional study), and also with the onset of hypertension (longitudinal study). Furthermore, one interesting report shows that treatment of hyperuricemia with allopurinol lowers blood pressure in juvenile essential hypertension patients with hyperuricemia. In addition, it is well known that hyperuricemia is closely associated with chronic kidney disease (CKD), is a risk factor for renal insufficiency in general populations, and is a poor prognostic factor of renal function in patients who also have IgA nephropathy. On the other hand, in intervention studies on hyperuricemia, the treatment of hyperuricemia with allopurinol in CKD has resulted in a fall in blood pressure and inhibition of the progression of renal damage. Conversely, the cessation of allopurinol treatment in CKD was followed by a rise in blood pressure and the development of renal damage. Furthermore, the rise of blood pressure and development of renal damage following cessation of allopurinol treatment are only seen in patients not receiving angiotensin converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB). This suggests that the renin angiotensin (RA) system plays an important role in the development of hypertension and renal damage from hyperuricemia.     

Effect of Naturally Occurring Flavonoids on Lipid Peroxidation and Membrane Permeability Transition in Mitochondria

The ability of eight structurally related naturally occurring flavonoids in inhibiting lipid peroxidation and mitochondrial membrane permeability transition (MMPT), as well as respiration and protein sulfhydryl oxidation in rat liver mitochondria, was evaluated. The flavonoids tested exhibited the following order of potency to inhibit ADP/Fe(II)-induced lipid peroxidation, estimated with the thiobarbituric acid assay: 3′-O-methyl-quercetin > quercetin > 3,5,7,3′,4′-penta-O-methyl-quercetin > 3,7,3′,4′-tetra-O-methyl-quercetin > pinobanksin > 7-O-methyl-pinocembrin > pinocembrin > 3-O-acyl-pinobanksin. MMPT was estimated by the extent of mitochondrial swelling induced by 10 μM CaCl₂ plus 1.5 mM inorganic phosphate or 30 μM mefenamic acid. The most potent inhibitors of MMPT were quercetin, 7-O-methyl-pinocembrin, pinocembrin, and 3,5,7,3′,4′-penta-O-methyl-quercetin. The first two inhibited in parallel the oxidation of mitochondrial protein sulfhydryl involved in the MMPT mechanism. The most potent inhibitors of mitochondrial respiration were 7-O-methyl-pinocembrin, quercetin, and 3′-O-methyl-quercetin while the most potent uncouplers were pinocembrin and 3-O-acyl-pinobanksin. In contrast 3,7,3′,4′-tetra-O-methyl-quercetin and 3,5,7,3′,4′-penta-O-methyl-quercetin showed the lowest ability to affect mitochondrial respiration. We conclude that, in general, the flavonoids tested are able to inhibit lipid peroxidation on the mitochondrial membrane and/or MMPT. Multiple methylation of the hydroxyl substitutions, in addition to sustaining good anti-lipoperoxidant activity, reduces the effect of flavonoids on mitochondrial respiration, and therefore, increases the pharmacological potential of these compounds against pathological processes related to oxidative stress.     

Syntheses of Naturally Occurring Terphenyls and Related Compounds

Naturally occurring terphenyls and related compounds such as terferol and its corresponding quinone and phlebiarubrone were synthesized from 2,5-diphenyl-1,4-benzoquinone. According to the proposed biosynthetic pathway, chemical conversion of phlebiarubrone to ustalic acid, a toxic compound isolated from the poisonous mushroom, Tricholoma ustale, was examined to find a low-yield conversion to the ustalic acid dimethyl ester.     

Comparative Mechanical Properties and Histology of Bone

Different bone tissues differ in their amounts of porosity,mineralization,reconstruction, and preferred orientation. Allthese have important effects on mechanical properties. Veryporous, cancellous bone is always weaker and morecompliant thancompact bone on a weight for weight basis, yet it occurs inplaceswhere its energyabsorbing ability, or its low density,is advantageous. Bonevaries considerably in its mineralization,and such variations have quite disproportionate effects on mechanicalproperties. These variations can be shown to be adaptive. Inparticular, there must always be a compromise between stiffnessandresistanceto fracture; these two properties run contrary to each other.The reason for secondary remodeling is an unresolved problem,though in a few places the role of such remodeling in changingthe grain of the bone is clearly mechanically adaptive. Themechanical properties of non-mammalian bone are obscure, andas the histology of such bone is often quite different fromthat of mammalian bone, we are no doubt in for some surpriseswhen the mechanical properties ofnonmammalian bone are discovered.     

Effect of Naturally Occurring Xanthines on Bacteria: I. Antimicrobial Action and Potentiating Effect on Antibiotic Spectra

The effect of xanthines on various microorganisms was studied. The antibacterial effect was not high; most of the test organisms could easily withstand a concentration of 2,500 μg/ml. Caffeine was more antibacterial than theophylline, and the latter more than theobromine. Caffeine citrate exhibited greater inhibitory effect than did pure caffeine. The effect was both bacteriostatic and bactericidal against susceptible organisms. The susceptibility of organisms to xanthines differed greatly even in related species. The morphology of Aerobacter aerogenes and A. cloacae was affected under the influence of caffeine; filamentation of cells followed sublethal doses. Potentiation was seen with antibiotics and caffeine; resistant strains were killed with a lower dose of drug in the presence of caffeine. This potentiating effect was pronounced with the tetracyclines; with streptomycin, the effect was the contrary.     

Prevention of Chronic Kidney Disease and Subsequent Effect on Mortality: A Systematic Review and Meta-Analysis

Objectives

To perform a systematic review of randomized controlled trials to determine whether prevention or slowing of progression of chronic kidney disease would translate into improved mortality, and if so, the attributable risk due to CKD itself on mortality.

Background

CKD is associated with increased mortality. This association is largely based on evidence from the observational studies and evidence from randomized controlled trials is lacking.

Methods

We searched Ovid, Medline and Embase for RCTs in which an intervention was given to prevent or slow the progression of CKD and mortality was reported as primary, secondary or adverse outcomes were eligible and selected. For the first phase, pooled relative risks for renal endpoints were assessed. For the second phase, we assessed the effect on mortality in trials of interventions that definitively reduced CKD endpoints.

Results

Among 52 studies selected in first phase, only renin-angiotensin-aldosterone-system blockade vs. placebo (n = 18 trials, 32,557 participants) met the efficacy criteria for further analysis in the second phase by reducing renal endpoints 15 to 27% compared to placebo. There was no difference in all-cause mortality (RR 0.99, 95% CI 0.92 to 1.08) or CV death (RR 0.97, 95% CI 0.78 to 1.21) between the treatment and control groups in these trials. There was sufficient statistical power to detect a 9% relative risk reduction in all-cause mortality and a 14% relative risk reduction in cardiovascular mortality.

Conclusions

Firm evidence is lacking that prevention of CKD translates into reductions in mortality. Larger trials with longer follow-up time are needed to determine the benefit of CKD prevention on survival.     

Biosynthesis of the Naturally Occurring Nucleoside Antibiotics from Adenosine

Abstract

9-β-D-Arabinofuranosyladenine (ara-A, l), first isolated from the culture filtrates of StreDtomyces antibioticus, has a broad spectrum of activity against DNA viruses in cell culture and is successfully used in therapy of herpes simplex encephalitis, neonatal herpes, herpes zoster and chronic myelogenous leukemia¹. 2′-Chlorodeoxycoformycin (2′CldCF, 2), 2′-amino-Zt-deoxyadenosine (3) and nucleocidin (4) have been isolated from the culture medium of Fctinomadura and S. clavus, respectively.     

Serum Uric Acid and Chronic Kidney Disease: The Role of Hypertension

Background

There are inconsistent findings on the role of hyperuricemia as an independent risk factor for chronic kidney disease (CKD). Hypertension has been implicated as a factor influencing the association between serum uric acid and CKD. In this population-based study we investigated the association between serum uric acid and decline in renal function and tested whether hypertension moderates this association.

Methods

We included 2601 subjects aged 55 years and over from the Rotterdam Study. Serum uric acid and estimated glomerular filtration rate (eGFR) were assessed at baseline. After average 6.5 years of follow-up, second eGFR was assessed. CKD was defined as eGFR<60 ml/min/1.73 m². All associations were corrected for socio-demographic and cardiovascular factors.

Results

Each unit (mg/dL) increase in serum uric acid was associated with 0.19 ml/min per 1.73 m² faster annual decline in eGFR. While the association between serum uric acid and incidence of CKD was not significant in our study population (Hazard Ratio: 1.12, 95% confidence interval [CI]: 0.98–1.28), incorporating our results in a meta-analysis with eleven published studies revealed a significant association (Relative Risk: 1.18, 95%CI: 1.15–1.22). In the stratified analyses, we observed that the associations of serum uric acid with eGFR decline and incident CKD were stronger in hypertensive subjects (P for interaction = 0.046 and 0.024, respectively).

Conclusions

Our findings suggest that hyperuricemia is independently associated with a decline in renal function. Stronger association in hypertensive individuals may indicate that hypertension mediates the association between serum uric acid and CKD.     

脂肪因子在慢性肾脏病血管钙化中的作用

慢性肾脏病(chronic kidney disease, CKD)是一种全球性的经济成本高的健康负担。慢性肾脏病首要的死亡并发症是心血管疾病(cardiovascular disease, CVD),而血管钙化是引起慢性肾脏病患者发生心血管疾病的主要原因。当体内的促钙化因子与抑钙化因子失衡时,会激活血管内皮细胞一系列反应,从而促进血管钙化。最近研究发现在慢性肾脏病血管钙化的发生、发展过程中,脂肪因子扮演着重要角色。本文对各种脂肪因子在慢性肾脏病血管钙化中的作用进行详细的阐述,希望可以为慢性肾脏病血管钙化的防治提供新思路。     

A Pharmaco-Metabonomic Study on Chronic Kidney Disease and Therapeutic Effect of Ergone by UPLC-QTOF/HDMS

Chronic kidney disease (CKD) is an important public health problem. Ergone has been proved to prevent the progression of CKD. UPLC-QTOF/HDMS was employed for metabolic profiling of adenine-induced CKD and to investigate the nephroprotective effects of ergone. Pharmacology parameters including blood biochemistry, histopathological evaluation and Western blot analysis were performed concurrently. The UPLC-MS data were analyzed by partial least squares-discriminate analysis, correlation analysis, heatmap analysis and mapped to KEGG pathways. Blood and serum biochemistry were observed to be significantly different in the CKD group than in the control group. In conjunction with biochemistry, histopathology and protein expression results, identified metabolites indicated perturbations in fatty acid metabolism, purine metabolism and amino acid metabolism as changes associated with adenine-induced CKD and the interventions of ergone. Upregulated expression of TGF-β1, ED-1, CTGF, bFGF and collagen I was observed in the CKD group. However, downregulated expression of these proteins was observed after oral administration of ergone. These results suggest that expression changes in these proteins had implications for fatty acid metabolism, purine metabolism and amino acid metabolism in the development of CKD and that ergone treatment could delay the development of CKD by normalizing or blocking abnormal changes in biomarker metabolites and protein expression in the CKD group.