Urinary Protein Profiling for Potential Biomarkers of Chronic Kidney Disease: A Pilot Study

Distinct Urinary Proteome Changes Across Estimated Glomerular Filtration Rate Stages in a Cohort of Black South Africans

Kidney function parameters including estimated glomerular filtration rate (eGFR) and urine albumin excretion are commonly used to diagnose chronic kidney disease (CKD). However, these parameters are relatively insensitive, limiting their utility for screening and early detection of kidney disease. Studies have suggested that urinary proteomic profiles differ by eGFR stage, offering potential insights into kidney disease pathogenesis alongside opportunities to increase the sensitivity of current testing strategies. In this study, we characterized and compared the urinary proteome across different eGFR stages in a Black African cohort from rural Mpumalanga Province, South Africa. We stratified 81 urine samples by eGFR stage (mL/min/1.73 m2): Stage G1 (eGFR ≥ 90; n = 36), Stage G2 (eGFR 60-89; n = 35), and Stage G3-G5 (eGFR < 60; n = 10). Urine proteomic analysis was performed using an Evosep One liquid chromatography system coupled to a Sciex 5600 TripleTOF in data-independent acquisition mode. Nonparametric multivariate analysis and receiver operating characteristic (ROC) curves were used to assess the performance of differentially abundant proteins (DAPs). Pathway analysis was performed on DAPs. Creatinine-based eGFR was calculated using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation. In this study, thirty-eight urinary proteins were differentially abundant for eGFR Stages 3-5 when compared to Stages G1 (AUC = 0.95; CI: 0.86-1) and G2 (AUC = 0.84; CI: 0.64-0.98). Notably, only six urinary proteins (Cystatin M (CST6), glutathione hydrolase 6 (GGT6), sushi domain containing 2 (SUSD2), insulin-like growth factor binding protein 6 (IGFBP6), heat shock protein 90 beta family member 1 (HSP90B1), and mannosidase alpha class 1A member 1 (MAN1A1)) were differentially abundant when comparing Stage G1 and Stage G2 with a modest AUC = 0.81 (CI: 0.67-0.92). Pathway analysis indicated that DAPs were associated with haemostasis and fibrin clot formation. In a rural cohort from South Africa, the urinary proteome differed by eGFR stage, and we identified six differentially abundant proteins which, in combination, could help to differentiate earlier eGFR stages with higher predictive accuracy than the currently available tests.

Salivary proteomics profiling reveals potential biomarkers for chronic kidney disease: a pilot study

Introduction

Chronic kidney disease (CKD) is a global public health problem, and the absence of reliable and accurate diagnostic and monitoring tools contributes to delayed treatment, impacting patients' quality of life and increasing treatment costs in public health. Proteomics using saliva is a key strategy for identifying potential disease biomarkers.

Methods

We analyzed the untargeted proteomic profiles of saliva samples from 20 individuals with end-stage kidney disease (ESKD) (n = 10) and healthy individuals (n = 10) using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify potential biomarkers for CKD. A volcano plot was generated using a p-value of ≤0.05 and a fold change (FC) ≥ 2.0. Multivariate analysis was performed to generate the orthogonal partial least squares discriminant analysis (OPLS-DA) model and the variable importance in projection (VIP) scores. The accuracy of candidate biomarker proteins was evaluated using receiver operating characteristic (ROC) curves.

Results

In total, 431 proteins were identified in the salivary proteomic profile, and 3 proteins were significantly different between the groups: apoptosis inhibitor 5 (API5), phosphoinositide phospholipase C (PI-PLC), and small G protein signaling modulator 2 (Sgsm2). These proteins showed good accuracy based on the ROC curve and a VIP score of >2.0. During pathway enrichment, PI-PLC participates in the synthesis of IP3 and IP4 in the cytosol. Gene ontology (GO) analysis revealed data on molecular functions, biological processes, cellular components, and protein classes.

Conclusion

We can conclude that the salivary API5, PI-PLC, and Sgsm2 can be potential biomarker candidates for CKD detection. These proteins may participate in pathways related to renal fibrosis and other associated diseases, such as mineral and bone disorders.

Urinary Proteomic Shifts over Time and Their Associations with eGFR Decline in Chronic Kidney Disease

Chronic kidney disease (CKD) is a progressive condition characterized by declining renal function, with limited biomarkers to predict its progression. The early identification of prognostic biomarkers is crucial for improving patient care and therapeutic strategies. This follow-up study investigated urinary proteomics and clinical outcomes in 18 CKD patients (stages 1-3) and 15 healthy controls using liquid chromatography-mass spectrometry and Mascot-SwissProt for protein identification. The exponentially modified protein abundance index (emPAI) was used for peptide quantification. Regression analyses were used to evaluate relationships between urinary proteins and the estimated glomerular filtration rate (eGFR), adjusting for proteinuria. At baseline, 171 proteins (median emPAI 86) were identified in CKD patients, and 271 were identified (median emPAI 47) in controls. At follow-up, 285 proteins (median emPAI 44.8) were identified in CKD patients, and 252 were identified (median emPAI 34.2) in controls. FBN1 was positively associated with eGFR, while FETUA showed a significant negative correlation at baseline. At follow-up, VTDB shifted from a negative baseline to a positive association with eGFR over time. CD44 and FBN1 shifted from a positive baseline to a negative association over time. These findings highlight VTDB, FBN1, and CD44 as potential prognostic biomarkers, providing insights into CKD progression and therapeutic targets.

In Vivo Assessment of Individual and Total Proteinuria in Zebrafish Larvae Using the Solvatochromic Compound ZMB741

The robustness of blood filtration in the kidney is supported by two major functions: the molecular sieve of the glomerulus and reabsorption of the proximal tubules. Detecting glomerular dysfunction is challenging because of the compensatory nature of proximal tubule reabsorption. To facilitate pathophysiological studies of the vertebrate kidney, zebrafish pronephroi are used, owing to their simple glomerular and proximal tubular configuration. In this study, a solvatochromic dye with an affinity for plasma proteins was used to detect urinary proteins leaking into the ureter of zebrafish. Aristolochic acid exposure to fertilized eggs of transgenic zebrafish expressing green fluorescent protein from the proximal tubules to the excretory pore induced concentration-dependent renal dysfunction. The solvatochromic dye ZMB741 was applied via static immersion to analyze leaked dye-plasma-protein complexes in the ureter; their axial distribution was imaged by using confocal microscopy. The effect of resveratrol, an attenuator of aristolochic acid nephropathy, was further analyzed. This method enables individual-level analysis of podocytopathy, a mild glomerular disease that does not necessarily lead to the excretion of proteinuria. Moreover, it will be useful for pathophysiological studies of renal function and the identification of potential therapeutic drugs.

A pilot study on the differential urine proteomic profile of subjects with community-acquired acute kidney injury who recover versus those who do not recover completely at 4 months after hospital discharge

Background

Community-acquired acute kidney injury (CA-AKI) is a sudden structural damage and loss of kidney function in otherwise healthy individuals outside of hospital settings having high morbidity and mortality rates worldwide. Long-term sequelae of AKI involve an associated risk of progression to chronic kidney disease (CKD). Serum creatinine (SCr), the currently used clinical parameter for diagnosing AKI, varies greatly with age, gender, diet, and muscle mass. In the present study, we investigated the difference in urinary proteomic profile of subjects that recovered (R) and incompletely recovered (IR) from CA-AKI, 4 months after hospital discharge.

Methods

Study subjects were recruited from ongoing study of CA-AKI cohort. Patients with either sex or age > 18 years with no underline CKD were enrolled at the time of hospital discharge. Incomplete recovery from CA-AKI was defined as eGFR < 60 mL/min/1.73 m2 or dialysis dependence at 4 months after discharge. Second-morning urine samples were collected, and proteome analysis was performed with LC-MS/MS. Data were analyzed by Proteome Discoverer platform 2.2 (Thermo Scientific) using statistical and various bioinformatics tools for abundance of protein, cellular component, protein class and biological process were analyzed in the recovered and incompletely recovered groups.

Results

A total of 28 subjects (14 in each group) were enrolled. Collectively, 2019 peptides and proteins with 30 high-abundance proteins in the incompletely recovered group (R/IR <0.5, abundance ratio adj. p-value <0.05) and 11 high-abundance proteins in the incompletely recovered group (R/IR >2.0, abundance ratio adj. p-value <0.05) were identified. Tissue specificity analysis, GO enrichment analysis, and pathway enrichment analysis revealed significant proteins in both the groups that are part of different pathways and might be playing crucial role in renal recovery during the 4-month span after hospital discharge.

Conclusion

In conclusion, this study helped in identifying potential proteins and associated pathways that are either upregulated or downregulated at the time of hospital discharge in incompletely recovered CA-AKI patients that can be further investigated to check for their exact role in the disease progression or repair.

Candidate protein biomarkers in chronic kidney disease: a proteomics study

Proteinuria poses a substantial risk for the progression of chronic kidney disease (CKD) and its related complications. Kidneys excrete hundreds of individual proteins, some with a potential impact on CKD progression or as a marker of the disease. However, the available data on specific urinary proteins and their relationship with CKD severity remain limited. Therefore, we aimed to investigate the urinary proteome and its association with kidney function in CKD patients and healthy controls. The proteomic analysis of urine samples showed CKD stage-specific differences in the number of detected proteins and the exponentially modified protein abundance index for total protein (p = 0.007). Notably, specific urinary proteins such as B2MG, FETUA, VTDB, and AMBP exhibited robust negative associations with kidney function in CKD patients compared to controls. Also, A1AG2, CD44, CD59, CERU, KNG1, LV39, OSTP, RNAS1, SH3L3, and UROM proteins showed positive associations with kidney function in the entire cohort, while LV39, A1BG, and CERU consistently displayed positive associations in patients compared to controls. This study suggests that specific urinary proteins, which were found to be negatively or positively associated with the kidney function of CKD patients, can serve as markers of dysfunctional or functional kidneys, respectively.

Tubular toxicity of proteinuria and the progression of chronic kidney disease

Proteinuria is a well-established biomarker of chronic kidney disease (CKD) and a risk predictor of associated disease outcomes. Proteinuria is also a driver of CKD progression toward end-stage kidney disease. Toxic effects of filtered proteins on proximal tubular epithelial cells enhance tubular atrophy and interstitial fibrosis. The extent of protein toxicity and the underlying molecular mechanisms responsible for tubular injury during proteinuria remain unclear. Nevertheless, albumin elicits its toxic effects when degraded and reabsorbed by proximal tubular epithelial cells. Overall, healthy kidneys excrete over 1000 individual proteins, which may be potentially harmful to proximal tubular epithelial cells when filtered and/or reabsorbed in excess. Proteinuria can cause kidney damage, inflammation and fibrosis by increasing reactive oxygen species, autophagy dysfunction, lysosomal membrane permeabilization, endoplasmic reticulum stress and complement activation. Here we summarize toxic proteins reported in proteinuria and the current understanding of molecular mechanisms of toxicity of proteins on proximal tubular epithelial cells leading to CKD progression.

Annual survival of patients with end-stage chronic kidney disease on supportive hemodialysis and its correlates

OBJECTIVE

Aim: The aim of the study was to determine the relationship of residual renal function, markers of inflammation and protein-energy expenditure with annual survival in patients undergoing hemodialysis.

PATIENTS AND METHODS

Materials and Methods: The work was a prospective cohort study and included 299 patient data. Residual kidney function was determined by urine volume of more than 250 ml per day to assess the effect. According to this criterion, the patients were divided into two groups. The degree of chronic inflammation was assessed by the content of acute phase proteins (ferritin and C-reactive protein) in the blood serum. The serum albumin level was chosen as a marker of protein-energy expenditure. The survival rate of patients with residual renal function was higher as compared to patients without it (p<0.001).

RESULTS

Results: In the current study, the absence of residual kidney function increased the risk of mortality from all causes in patients who had recently undergone hemodialysis by almost 30 times during the first year of substitution therapy. C-reactive protein was also associated with poorer survival in these patients (HR=1.01; 95% CI: 1-1.02), while albumin was inversely associated with mortality (HR=0.92; 95% CI: 0.87-0.98).

CONCLUSION

Conclusions: Thus, residual renal function and higher serum albumin levels by the time maintenance hemodialysis begins are independent predictors of the best survival during the first year of replacement therapy. The presence of residual kidney function of less than 250 ml and a higher level of C-reactive protein correlated with an increased risk of mortality in these patients.

Measurement of Urinary Gc-Globulin by a Fluorescence ELISA Technique: Method Validation and Clinical Evaluation in Septic Patients-A Pilot Study

A major complication of sepsis is the development of acute kidney injury (AKI). In case of acute tubular damage, Gc-globulin, a known serum sepsis marker is increasingly filtrated into the urine therefore, urinary Gc-globulin (u-Gc) levels may predict septic AKI. We developed and validated a competitive fluorescence ELISA method for u-Gc measurement. Serum and urine samples from septic patients were collected in three consecutive days (T1, T2, T3) and data were compared to controls. Intra- and interassay imprecisions were CV < 14% and CV < 20%, respectively, with a recovery close to 100%. Controls and septic patients differed (p < 0.001) in their u-Gc/u-creatinine levels at admission (T1, median: 0.51 vs. 79.1 µg/mmol), T2 (median: 0.51 vs. 57.8 µg/mmol) and T3 (median: 0.51 vs. 55.6 µg/mmol). Septic patients with AKI expressed higher u-Gc/u-creatinine values than those without AKI at T1 (median: 23.6 vs. 136.5 µg/mmol, p < 0.01) and T3 (median: 34.4 vs. 75.8 µg/mmol, p < 0.05). AKI-2 stage patients exhibited more increased u-Gc/u-creatinine levels at T1 (median: 207.1 vs. 53.3 µg/mmol, p < 0.05) than AKI-1 stage individuals. Moderate correlations (p < 0.001) were observed between u-Gc/u-creatinine and se-urea, se-creatinine, se-hsCRP, WBC, u-total protein, u-albumin, u-orosomucoid/u-creatinine, and u-Cystatin C/u-creatinine levels. U-Gc testing may have a predictive value for AKI in septic patients.