Novel plasma peptide markers involved in the pathology of CKD identified using mass spectrometric approach

Abstract

Chronic kidney disease (CKD) may progress to end-stage renal disease (ESRD) at different pace. Early markers of disease progression could facilitate and improve patient management. However, conventional blood and urine chemistry have proven unable to predict the progression of disease at early stages. Therefore, we performed untargeted plasma peptidome analysis to select the peptides involved in progression, which are suitable for long prospective studies in future. The study consists of non-CKD (n = 66) and CKD (n = 106) patients with different stages. We performed plasma peptidomics on these subjects using chromatography and mass spectrometric approaches. Initially, we performed LC-ESI-MS and applied least absolute shrinkage and selection operator logistic regressions to select the peptides that are differentially expressed and we generated a peptidomic score for each subject. Later, we identified and sequenced the peptides with MALDI-MS/MS and also performed univariate and multivariate analyses with the clinical variables and peptidomic score to reveal their association with progression of renal disease. A logistic regression model selected 14 substances showing different concentrations according to renal function, of which seven substances were most likely occur in CKD patients. The peptidomic model had a global P value of < 0.01 with R2 of 0.466, and the area under the curve was 0.87 (95% CI, 0.8149–0.9186; P < 0.0001). The predicted score was significantly higher in CKD than in non-CKD patients (2.539 ± 0.2637 vs − 0.9382 ± 0.1691). The model was also able to predict stages of CKD: the Spearman correlation coefficient of the linear predictor with CKD stages was 0.83 with concordance indices of 0.899 (95% CI 0.863–0.927). In univariate analysis, the most consistent association of peptidomic score in CKD patients was with C-reactive protein, sodium level, and uric acid, which are unanticipated substances. Peptidomic analysis enabled to list some unanticipated substances that have not been extensively studied in the context of CKD but were associated with CKD progression, thus revealing interesting candidate markers or mediators of CKD of potential use in CKD progression management.Key messages• Conventional blood and urine chemistry have proven unable to predict the progression of disease at early stages of chronic kidney disease (CKD).• We performed untargeted plasma peptidome analysis to select the peptides involved in progression.• A logistic regression model selected 14 substances showing different concentrations according to renal function.• These peptides are unanticipated substances that have not been extensively studied in the context of CKD but were associated with CKD progression, thus revealing markers or mediators of CKD of potential use in CKD progression management.

Sequential Precipitation and Delipidation Enables Efficient Enrichment of Low-Molecular Weight Proteins and Peptides from Human Plasma

“…Since LMWPs are small enough to readily enter the blood from different tissue locations, they are expected to be identified as disease-associated biomarkers. LMWPs have been implicated in various human diseases such as cancer, diabetes, and chronic kidney diseases and represent a treasure trove of diagnostic molecules. For example, the ratio of the amyloid-β precursor protein and amyloid-β fragments can be used for the diagnosis of Alzheimer’s disease …”

Effect of the transjugular intrahepatic portosystemic shunt on peptidomics composition of peripheral plasma

“…Since peptidomics is a powerful tool to discover and determine new biomarkers 23,24 as well as to identify novel peptides to be employed in prevention and prediction models 35 , we developed and applied a work ow to prepare, analyze and interpret peptidomics data by the employment of mass spectrometry and statistics to investigate the plasma of patients suffering from portal hypertension and liver diseases, comparing the molecular pro le before and after TIPS treatment to reduce portal hypertension. The peptidomics approach adopted in this study focused on identifying only features that showed to be signi cantly different between the two groups analysed (before and after TIPS treatment).…”

“…Peptidomics is a proteomics-derived branch of omics techniques and is based on liquid chromatographymass spectrometry (LC-MS) as an e cient method for targeted and non-targeted peptide identi cation in diseases 23,24 . LC-MS allows wide-spectrum analyses of the peptidome and metabolome and hence it has been successfully employed for the identi cation of biomarkers of various diseases 25 .…”

Peptidomics: A Review of Clinical Applications and Methodologies

“…Untargeted analyses are rare in clinical peptidomics but have successfully been used to identify early markers of disease progression for conditions such as chronic kidney disease. 150 Using acid precipitation and fractionation by reverse-phase chromatography, peptides were extracted from plasma from patients with various stages of kidney disease. By also analyzing control samples to generate linear prediction models, new potential biomarkers for the disease were identified.…”