Differential Urinary Proteome Analysis for Predicting Prognosis in Type 2 Diabetes Patients with and without Renal Dysfunction.

Renal dysfunction, a major complication of type 2 diabetes, can be predicted from estimated glomerular filtration rate (eGFR) and protein markers such as albumin concentration. Urinary protein biomarkers may be used to monitor or predict patient status. Urine samples were selected from patients enrolled in the retrospective diabetic kidney disease (DKD) study, including 35 with good and 19 with poor prognosis. After removal of albumin and immunoglobulin, the remaining proteins were reduced, alkylated, digested, and analyzed qualitatively and quantitatively with a nano LC-MS platform. Each protein was identified, and its concentration normalized to that of creatinine. A prognostic model of DKD was formulated based on the adjusted quantities of each protein in the two groups. Of 1296 proteins identified in the 54 urine samples, 66 were differentially abundant in the two groups (area under the curve (AUC): p-value < 0.05), but none showed significantly better performance than albumin. To improve the predictive power by multivariate analysis, five proteins (ACP2, CTSA, GM2A, MUC1, and SPARCL1) were selected as significant by an AUC-based random forest method. The application of two classifiers-support vector machine and random forest-showed that the multivariate model performed better than univariate analysis of mucin-1 (AUC: 0.935 vs. 0.791) and albumin (AUC: 1.0 vs. 0.722). The urinary proteome can reflect kidney function directly and can predict the prognosis of patients with chronic kidney dysfunction. Classification based on five urinary proteins may better predict the prognosis of DKD patients than urinary albumin concentration or eGFR.

Elevated Levels of Urinary Extracellular Vesicle Fibroblast-Specific Protein 1 in Patients with Active Crescentic Glomerulonephritis.

BACKGROUND/AIMS: Extracellular vesicles (EVs), including exosomes, are present in various bodily fluids, including urine. We and others previously reported that cells expressing fibroblast-specific protein 1 (FSP1) accumulate within damaged glomeruli, and that urinary FSP1, as well as urinary soluble CD163, could potentially serve as a biomarker of ongoing glomerular injury. METHODS: To test that idea, we collected urine samples from 37 patients with glomerular disease; purified the urinary EVs; characterized them using Nanosight, western blotting, and immunoelectron microscopy; and determined FSP1 and soluble CD163 levels using enzyme-linked immunosorbent assays. RESULTS: Deemed to be mainly exosomes based on their size distribution, the EVs in urine contained FSP1, and a portion of the FSP1-positive vesicles was also positive for podocalyxin. FSP1 levels in urinary EVs were (1) positively correlated with rates of biopsy-proven cellular crescent formation (r = 0.562, p < 0.001) and total crescent formation (r = 0.448, p = 0.005) among total glomeruli; (2) significantly higher in patients with cellular crescents affecting 20% or more of their glomeruli than in those with fewer affected glomeruli (p = 0.003); and (3) significantly decreased after glucocorticoid and immunosuppressant therapy (p < 0.05). A positive correlation between FSP1 levels in urinary EVs and urinary soluble CD163 levels was confirmed (r = 0.367, p < 0.05). CONCLUSION: These data suggest that a portion of urinary FSP1 is secreted as EVs originating from podocytes, and that FSP1 levels reflect active and ongoing glomerular injury and disease activity, such as cellular crescent formation.

Characterization of urinary exosomal release of aquaporin-1 and -2 after renal ischemia-reperfusion in rats.

Acute kidney injury (AKI) is an important risk factor for the development of chronic kidney disease (CKD), and an alteration in renal water handling has been observed during the transition of AKI to CKD. Urinary exosomal release of aquaporin-1 (AQP1) and AQP2, important proteins for renal water handling, has recently been reported to predict their levels of renal expression. Therefore, we examined the patterns of urinary exosomal release of AQP1 and AQP2, and the exosomal marker proteins tumor susceptibility 101 protein (TSG101) and ALG-2 interacting protein X (Alix), in the acute and chronic phases following induction of AKI by renal bilateral ischemia/reperfusion (I/R) in rats. Blood tests and histological examinations indicated that AKI occurred before at 7 days after renal I/R ( day 7) and that renal fibrosis developed progressively thereafter. Immunoblotting demonstrated significant decreases in the urinary exosomal release of AQP1 and AQP2 during severe AKI. Urinary exosomal release of Alix and TSG101 was significantly increased on day 7. These data were also confirmed in rats with unilateral renal I/R causing more serious AKI. Urinary exosomal release of either the Ser-256- or Ser-269-phosphorylated form of AQP2, both of which are involved in apical trafficking of AQP2, was positively correlated with that of total AQP2. These results suggest that urinary exosomal release of AQP1 and AQP2 is reduced in I/R-induced AKI, whereas that of Alix and TSG101 is increased in the initial phase of renal fibrosis. Furthermore, apical trafficking of AQP2 appears to be related to urinary exosomal release of AQP2.

Research on the correlation of urine calcium integrin binding protein-1 and pro-BNP with ischemic heart failure.

OBJECTIVE: To investigate the correlation between the levels of urine calcium integrin binding protein-1 (CIB1) and serum precursor N-terminal brain natriuretic peptide (pro-BNP) and ischemic heart failure. PATIENTS AND METHODS: 30 patients diagnosed as acute ischemic heart failure for the first time in our hospital from January to August 2016 were continuously selected as the observation group 1, 30 patients with chronic stable ischemic heart failure as the observation group 2, and 30 healthy volunteers as the control group. Urine CIB1 level was detected via enzyme linked immunosorbent assay (ELISA) and serum pro-BNP level was detected via radioimmunoassay. The linear correlation between the CIB1 and pro-BNP levels in observation group 1 was observed, and the diagnostic value of CIB1 and pro-BNP levels for chronic stable ischemic heart failure were analyzed using the receiver operating characteristic (ROC) curve. RESULTS: CIB1 and pro-BNP levels in the observation group 1 were significantly higher than those in the observation group 2. These levels were significantly lower in the control group (p < 0.05). In the observation group 1, CIB1 and pro-BNP levels were positively correlated (p < 0.05). The diagnostic accuracy of CIB1 for chronic stable ischemic heart failure in the observation group 2 (area under the curve, AUC) was 0.854, the sensitivity was 86.6% and the specificity was 82.5%, respectively. The diagnostic accuracy of pro-BNP was 0.823, the sensitivity was 83.5% and the specificity was 85.9%, respectively. CONCLUSIONS: There is a significant correlation between the urine CIB1 and serum pro-BNP levels in patients with acute ischemic heart failure. In patients with chronic stable ischemic heart failure, the diagnostic value of urine CIB1 outperforms that of serum pro-BNP, which still needs further study.

Effect of pH on the isolation of urinary exosome.

PURPOSE: Urinary exosome is an ideal noninvasive, low-cost source of kidney diseases biomarkers. However, many factors effect the isolation of urine-derived exosome. The effect of pH on the yield of exosome isolation under different pH was explored. METHODS: The pH was adjusted for 4, 5, 6, 7 and 8 with hydrochloric acid and sodium hydroxide solution. All samples were incubated for 30 min before differential ultracentrifugation. Exosome-associated protein markers TSG101, ALIX and total concentration of RNA were evaluated by Western-blotting and micro-amount ultraviolet spectrophotometer, respectively. RESULTS: A major loss of urinary exosome was received at pH 8 compared with alkali medium or control group. There was no difference whether or not added EDTA-Na2. CONCLUSIONS: Acidic environment was likely to conducive to the isolation of exosome and maintain its stability and integrity that suggest pH medium needs to be carefully considered and also provide a methodology for future separation exosome.

Urinary extracellular vesicles as reservoirs of altered proteins during the pathogenesis of polycystic kidney disease.

PURPOSE: Recent findings indicate that urinary extracellular vesicles (EVs) might reflect the pathophysiological state of urinary system; and that EVs-induced ciliary signaling is a possible mechanism of intercellular communication within the tract. Here, we aimed to analyze the protein expression of urinary EVs during autosomal dominant polycystic kidney disease (ADPKD). EXPERIMENTAL DESIGN: EVs were isolated from pooled urine samples of healthy control and ADPKD patients at two different stages of the disease and under tolvaptan treatment using the double-cushion ultracentrifugation method. Proteins were identified and quantified by iTRAQ and multidimensional protein identification technology (MudPIT)-based quantitative proteomics. RESULTS: Quantitative analyses identified 83 differentially expressed EV proteins. Many of these have apical membrane origin and are involved in signal transduction pathways of primary cilia, Ca(2+) -activated signaling, cell-cycle regulation, and cell differentiation. CONCLUSIONS AND CLINICAL RELEVANCE: The reduced AQP-2 and the increased APO-A1 levels observed in all ADPKD-affected groups may reflects the impaired renal concentrating capability of these patients and correlated with estimated glomerular filtration rate decline. The levels of some upregulated proteins involved in Ca(2+) -activated signaling declined upon tolvaptan treatment. The results obtained suggest that the quantitative proteomics of urinary EVs might be useful to monitor proteins difficult to access noninvasively, and thus advance our understanding of urinary tract physiology and pathology.

Programmed cell death 6 interacting protein (PDCD6IP) and Rabenosyn-5 (ZFYVE20) are potential urinary biomarkers for upper gastrointestinal cancer.

PURPOSE: Cancer of the upper digestive tract (uGI) is a major contributor to cancer-related death worldwide. Due to a rise in occurrence, together with poor survival rates and a lack of diagnostic or prognostic clinical assays, there is a clear need to establish molecular biomarkers. EXPERIMENTAL DESIGN: Initial assessment was performed on urine samples from 60 control and 60 uGI cancer patients using MS to establish a peak pattern or fingerprint model, which was validated by a further set of 59 samples. RESULTS: We detected 86 cluster peaks by MS above frequency and detection thresholds. Statistical testing and model building resulted in a peak profiling model of five relevant peaks with 88% overall sensitivity and 91% specificity, and overall correctness of 90%. High-resolution MS of 40 samples in the 2-10 kDa range resulted in 646 identified proteins, and pattern matching identified four of the five model peaks within significant parameters, namely programmed cell death 6 interacting protein (PDCD6IP/Alix/AIP1), Rabenosyn-5 (ZFYVE20), protein S100A8, and protein S100A9, of which the first two were validated by Western blotting. CONCLUSIONS AND CLINICAL RELEVANCE: We demonstrate that MS analysis of human urine can identify lead biomarker candidates in uGI cancers, which makes this technique potentially useful in defining and consolidating biomarker patterns for uGI cancer screening.

The urinary proteome and metabonome differ from normal in adults with mitochondrial disease.

We studied the extent and nature of renal involvement in a cohort of 117 adult patients with mitochondrial disease, by measuring urinary retinol-binding protein (RBP) and albumin; established markers of tubular and glomerular dysfunction, respectively. Seventy-five patients had the m.3243A>G mutation and the most frequent phenotypes within the entire cohort were 14 with MELAS, 33 with MIDD, and 17 with MERRF. Urinary RBP was increased in 29 of 75 of m.3243A>G patients, whereas albumin was increased in 23 of the 75. The corresponding numbers were 16 and 14, respectively, in the 42 non-m.3243A>G patients. RBP and albumin were higher in diabetic m.3243A>G patients than in nondiabetics, but there were no significant differences across the three major clinical phenotypes. The urine proteome (mass spectrometry) and metabonome (nuclear magnetic resonance) in a subset of the m.3243A>G patients were markedly different from controls, with the most significant alterations occurring in lysosomal proteins, calcium-binding proteins, and antioxidant defenses. Differences were also found between asymptomatic m.3243A>G carriers and controls. No patients had an elevated serum creatinine level, but 14% had hyponatremia, 10% had hypophosphatemia, and 14% had hypomagnesemia. Thus, abnormalities in kidney function are common in adults with mitochondrial disease, exist in the absence of elevated serum creatinine, and are not solely explained by diabetes.

Citrin deficiency in a Romanian child living in Spain highlights the worldwide distribution of this defect and illustrates the value of nutritional therapy.

We report citrin deficiency in a neonatal non-East-Asian patient, the ninth Caucasian reported with this disease. The association of intrahepatic cholestasis, galactosuria, very high alpha-fetoprotein and increased plasma and urine citrulline, tyrosine, methionine and threonine levels suggested citrin deficiency. Identification of a protein-truncating mutation (c.1078C>T; p.Arg360*) in the SLC25A13 gene confirmed the diagnosis. An immediate response to a high-protein, lactose-free, low-carbohydrate formula was observed. Our report illustrates the need for awareness on citrin deficiency in Western countries.

Urinary FSP1 is a biomarker of crescentic GN.

Fibroblast-specific protein 1 (FSP1)-expressing cells accumulate in damaged kidneys, but whether urinary FSP1 could serve as a biomarker of active renal injury is unknown. We measured urinary FSP1 in 147 patients with various types of glomerular disease using ELISA. Patients with crescentic GN, with or without antinuclear cytoplasmic antibody-associated GN, exhibited elevated levels of urinary FSP1. This assay had a sensitivity of 91.7% and a specificity of 90.2% for crescentic GN in this sample of patients. Moreover, we found that urinary FSP1 became undetectable after successful treatment, suggesting the possible use of FSP1 levels to monitor disease activity over time. Urinary FSP1 levels correlated positively with the number of FSP1-positive glomerular cells, predominantly podocytes and cellular crescents, the likely source of urinary FSP1. Even in patients without crescent formation, patients with high levels of urinary FSP1 had large numbers of FSP1-positive podocytes. Taken together, these data suggest the potential use of urinary FSP1 to screen for active and ongoing glomerular damage, such as the formation of cellular crescents.

Design and validation of an immunoaffinity LC-MS/MS assay for the quantification of a collagen type II neoepitope peptide in human urine: application as a biomarker of osteoarthritis.

Biomarkers play an increasingly important role for drug efficacy and safety evaluation in all stages of drug development. It is especially important to develop and validate sensitive and selective biomarkers for diseases where the onset of the disease is very slow and/or the disease progression is hard to follow, i.e., osteoarthritis (OA). The degradation of Type II collagen has been associated with the disease state of OA. Matrix metalloproteinases (MMPs) are enzymes that catalyze the degradation of collagen and therefore pursued as potential targets for the treatment of OA. Peptide biomarkers of MMP activity related to type II collagen degradation were identified and the presence of these peptides in MMP digests of human articular cartilage (HAC) explants and human urine were confirmed. An immunoaffinity LC/MS/MS assay for the quantification of the most abundant urinary type II collagen neoepitope (uTIINE) peptide, a 45-mer with 5 HO-proline residues was developed and clinically validated. The assay has subsequently been applied to analyze human urine samples from clinical studies. We have shown that the assay is able to differentiate between symptomatic OA and normal subjects, indicating that uTIINE can be used as potential biomarker for OA. This chapter discusses the assay procedure and provides information on the validation experiments used to evaluate the accuracy, precision, and selectivity data with attention to the specific challenges related to the quantification of endogenous protein/peptide biomarker analytes. The generalized approach can be used as a follow-up to studies whereby proteomics-based urinary biomarkers are identified and an assay needs to be developed. Considerations for the validation of such an assay are described.

Exosomes in urine: who would have thought...?

Normal urine contains thousands of proteins, largely due to the presence of 'exosomes,' tiny vesicles secreted into the urine by renal epithelial cells. These exosomes, demonstrated by Keller and colleagues to be also retrievable from amniotic fluid, offer great promise for future disease biomarker discovery studies.

Urinary excretion of epidermal-type fatty acid-binding protein and S100A7 protein in patients with cutaneous melanoma.

Epidermal-type fatty acid-binding protein (E-FABP), a protein related to the intracellular trafficking of fatty acids, is expressed in melanocytic tumours but not in normal human melanocytes. E-FABP interacts with S100A7. The presence of these two proteins was investigated in the urine of patients with cutaneous melanoma or other types of cancer, and healthy controls. The first voided morning urine samples of 31 patients with melanoma, 73 patients with other types of cancer and 17 healthy controls were concentrated and submitted to sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) immunoblotting for protein detection. In the healthy controls, the incidences of urinary detection of these proteins were higher in females than in males, being 50% (five out of 10) versus 0% (zero out of seven) for E-FABP ( < 0.05), and 70% (seven out of 10) versus 0% (zero out of seven) for S100A7 ( < 0.05). Both proteins were detected in the urine of patients with melanoma. The incidence of S100A7 was higher in the urine of patients with melanoma (77%, 24 out of 31) compared with healthy controls (41%, seven out of 17) and patients with other types of cancer (53%, 39 out of 73) ( < 0.03). In contrast, the incidence of E-FABP was the same among the melanoma group (39%, 12 out of 31), healthy controls (29%, five out of 17) and patients with other types of cancer (23%, 17 out of 73). Surprisingly, E-FABP was always detected in the urine of females with stage I/II or III melanoma, but was no longer detectable in the urine of patients with stage IV melanoma. Urinary S100A7 may have some specificity to the host response to melanoma since its incidence was not increased in other cancers. The lack of E-FABP detection in the urine of patients with distant metastases suggests an inverse relationship between E-FABP release and the spread of melanoma.

Restricted expression of calcium-binding protein S100A5 in human kidney.

Reverse transcription--polymerase chain reaction (RT-PCR) identified the expression of calcium-binding protein S100A5 in the noncancerous parts of resected samples from renal cell carcinoma (RCC) patients (n = 7) but not in the carcinoma lesions. Rabbit anti-S100A5 antibody immunohistochemically detected the antigen in the thick ascending limb of Henle, distal convoluted tubule, and collecting duct system. No apparent immunopositivity was observed in the glomerulus, proximal tubules, interstitial cells, or RCC cells. Thus, it was suggested that S100A5 protein plays an inherent functional role to the post-thick ascending limb of Henle portion in the nephron. Further, the carcinomas tested were originated probably not in the S100A5-positive distal epithelium but in the -negative epithelium of proximal tubules. Then, total RNA was extracted by phenol/chloroform from 1 ml urine of healthy volunteers, and S100A5 was amplified by RT-PCR from all samples (n = 12), indicating that the transcript of S100A5 is detectable even in the cells released into urine.

Mannan-binding lectin (MBL)-associated plasma protein present in human urine inhibits calcium oxalate crystal growth.

Mannan-binding lectin (MBL)-associated plasma protein (MAp19) is an alternatively spliced form of MBL-associated serine protease-2, a component of a complement activation cascade. We observed that MAp19 is excreted in human urine. Interestingly, the amount of MAp19 was higher in urine of renal cell carcinoma patients than healthy people. Pretreatment of urine dialysate with 50 mM EDTA increased the recovery of MAp19, suggesting that MAp19 is a calcium-binding protein. The recombinant MAp19 showed a strong inhibition of calcium oxalate crystal growth in vitro in a concentration-dependent manner. Thus, we conclude that MAp19 plays a role in the inhibition of calcium oxalate renal stone formation.

Psoriasin (S100A7): a putative urinary marker for the follow-up of patients with bladder squamous cell carcinomas.

To search for bladder squamous cell carcinoma markers that are released to the urine a blind and systematic analysis of the protein profiles of fresh tumors, their secreted proteins, as well as the patient's urine was carried out using state-of-the-art proteomic technology. We review the data concerning the putative marker psoriasin (S100A7), which, alone or in combination with other biomarkers, may be valuable for the noninvasive follow-up of patients bearing these tumors.

The epidermal growth factor precursor. A calcium-binding, beta-hydroxyasparagine containing modular protein present on the surface of platelets.

Various human body fluids and secretions contain a soluble form of the epidermal growth factor (EGF) precursor. The EGF precursor molecule contains eight EGF modules in addition to EGF itself. Using monoclonal antibodies specific for the EGF modules 7 and 8, we have purified the soluble form of the EGF precursor from human urine to homogeneity. The protein was shown to have a molecular mass of about 160 kDa and the N-terminal sequence SAPNHWSXPE. EGF modules 2, 7 and 8 of the precursor have the consensus sequence for post-translational beta-hydroxylation of Asp/Asn residues. We identified the presence of erythro-beta-hydroxy-aspartic acid (Hya) in acid hydrolysates of the EGF precursor (2.4 M.M protein-1). As the DNA sequence encodes Asn in the corresponding position, the Hya represents erythro-beta-hydroxyasparagine (Hyn). The Hyn-containing modules have a consensus calcium-binding motif immediately N-terminal of the first Cys residue. The synthetic EGF module 2 (residues 356-395) of the EGF precursor was found to bind calcium with low affinity, Kd approximately 3.5 mM, i.e. similar to the affinity of other isolated calcium-binding EGF modules. EGF module 7, when part of the intact protein, was found to bind Ca2+ with a Kd approximately 0.2 microM, i.e. approximately 10(4)-fold higher than that of isolated EGF modules presumably due to the influence of neighboring modules. We have detected EGF precursor in platelet-rich plasma and demonstrated it to be associated to platelets. The platelets were found to have 30-160 EGF molecules each.