Urinary Peptidomic Analysis Identifies Potential Biomarkers for Acute Rejection of Renal Transplantation
© Humana Press 2009
Received: 5 February 2009
Accepted: 3 April 2009
Published: 28 April 2009
Human urine is a complex matrix of proteins, endogenous peptides, lipids, and metabolites. The level of any or all of these components can reflect the pathophysiological status of an individual especially of the kidney at the time of urine collection. The naturally occurring endogenous urinary peptides which are thought to be the product of several proteolytic and degradation processes may provide clinically useful biomarkers for different renal and systemic diseases.
Materials and Methods
To examine if specific differences in the urinary peptidome (<10 kDa) occur at the time of acute renal transplant rejection (AR), we undertook a study of urine samples collected from biopsy-proven AR (n = 10), stable graft function (n = 10), and healthy normal control (n = 10). The peptides (<10 kDa) were extracted and fractionated with high-performance liquid chromatography followed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometric (MS) analysis.
We identified 54 endogenous peptides, including multiple peptides for Tamm–Horsfall protein (UMOD). A panel of peptides are identified which discriminate renal transplant patients with AR from stable graft. We have shown that liquid chromatography followed by MALDI is a useful tool to identify potential biomarkers, which after verification with larger patient cohort can be used as a non-invasive monitoring tool for renal transplant rejection.
KeywordsUrine Peptidomics Biomarker Renal transplantation Proteomics LC MALDI Urinary Peptidomics Acute rejection Non-invasive biomarkers Biomarker discovery
Urine is rich in proteins and peptides that could sample both renal as well as systemic events . Proteins and endogenous peptides resulting from processes that include glomerular filtration, apoptosis, and proteolytic degradations in urine may carry useful biomarkers for diseases including acute allograft rejection (AR) of renal transplant . AR is a primary risk factor for graft functional decline, chronic rejection, and accelerated graft loss [3, 4]. Elevations in the serum creatinine are nonspecific and may result from many causes of graft dysfunction (e.g., acute tubular necrosis, infection, drug toxicity), and AR can occur without an associated rise in the serum creatinine. The invasive biopsy, the current gold standard, correlates poorly with treatment response and prognosis and has associated complications of pain, sedation, hematuria, arteriovenous fistulae, graft thrombosis, and transfusion risk . Therefore, identification and validation of informative biomarkers for non-invasive monitoring for acute rejection is a critical unmet need in organ transplantation.
Urine has been analyzed to identify disease biomarkers for diseases including coronary artery disease , renal cell carcinoma , prostate cancer [8, 9], diabetes , and renal diseases [11–16]. The analysis of naturally occurring small molecular weight (MW) endogenous peptide analysis is termed as “peptidomics.” Techniques such as capillary-electrophoresis-coupled mass spectrometric analysis (CE MS) [17, 18], liquid chromatography (LC) MS with off-line coupled combination of reversed-phase high-performance liquid chromatography (HPLC) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF) , and magnetic bead separation followed by MALDI-TOF  have been used to study the urine peptidome. In this report, we develop and optimize a method to analyze endogenous urinary peptides ranging from 900 to 4,000 Da by label-free high-performance liquid chromatography coupled with MALDI-TOF analysis and identified potential biomarker peptides for acute rejection.
Materials and Methods
No. of subjects
Mean GFR (mL/min/1.73 m2)
12 ± 5
83.3 ± 52.2
12 ± 5
8 ± 4
Urine Collection, Initial Processing, and Storage
Fifty to 100 mL urine, collected in sterile containers, was centrifuged at 2,000×g for 20 min at room temperature within 1 h of collection. The supernatant was separated from the pellet containing any particulate matter including cells and cell debris. The pH of the supernatant was adjusted to 7.0 and stored at −80°C until further analysis.
Recovery and Quantification of Urinary Protein
Extraction of Low-MW Endogenous Peptides
The filtrates containing the low-MW urinary endogenous peptides were extracted with Waters® Oasis® HLB Extraction Cartridges (Waters Corporation, Milford, MA, USA). Briefly, the cartridges were activated with 2 mL 100% acetonitrile followed by equilibration with 5 mL 0.1% trifluoroacetic acid in water. The pH of the sample was adjusted to pH 3.0 by addition of 50% trifluoroacetic acid (TFA) and passed through the cartridge with 10 mL/min flow rate. The cartridge was washed with 5 mL 0.1% TFA in water and eluted with 3 mL 70% acetonitrile/0.1%TFA (flow rate no faster than 10 mL/min). The volume of the eluted peptides was brought to 0.5 mL by the use of SpeedVac. The peptides were extracted with 1 mL ethyl acetate by vortexing for 1 min. The aqueous layer was recovered by discarding the upper organic layer, and the volume of the extract was brought to 500 μL by SpeedVac centrifugation.
Quantification of Endogenous Peptides and Proteins
2,4,6-Trinitrobenzenesulfonic Acid Assay
The small-MW peptides were quantified using a method published elsewhere . Briefly, a standard curve was generated with glycine solution (10, 20, 30, 40, 50, 60, 70, 80 μM). Absorbance at 420 nm by 2,4,6-trinitrobenzenesulfonic acid (TNBS) was measured.
Urine creatinine was measured using Quantichrom™ Creatinine Assay Kit (DICT-500) (BioAssay Systems, Hayward, CA, USA). The manufacturer’s manual was followed for the assay.
Protein assay and Normalization
The large-MW protein fraction was quantified by bicinchoninic acid protein assay (Pierce, Rockford, IL, USA). We used 2,4,6-trinitrobenzenesulfonic acid assay to normalize the peptide load onto the LC fractionation. Since the samples have varied peptide concentration as measured by the TNBS assay, we created pools of samples to normalize for equal peptide content contribution from each individual sample. Aliquots containing 10 nmol were added from each individual samples in all the three phenotypes (AR, STA, and HC) to make a pool of 100 nmol peptides for each phenotype.
Three nanomoles peptides were injected on a 100 μm × 15 cm C18 reverse-phase column (Michrom) and eluted with a gradient of 5% to 55% acetonitrile over 50 min using a Michrom MS4 HPLC. Twenty-second fractions were collected onto MALDI targets with a Probot fraction collector (LC Packings). A total of 100 fractions were collected and analyzed on 4700 MALDI-TOF/TOF (Applied Biosystems) in MS mode. One microliter of matrix solution containing 4.8 mg/ml α-cyano-4-hydroxycinnamic acid (Agilent Technologies, Palo Alto, CA, USA and 30 fmol/μl glu-fibrinopeptide (Sigma-Aldrich, St. Louis, MO, USA) was automatically deposited by the Probot on each spot.
MS Data Collection and Analysis
Selected candidate biomarker peptides were analyzed by tandem mass spectrometry (MS/MS) using a 4700 MALDI-TOF/TOF (Applied Biosystems) in MS/MS mode. All MS/MS data were submitted for MASCOT database search for identification purpose. All positive peptides identified were manually reviewed.
After retrieving the signal intensities for the endogenous peptides from AR, STA, and HC, the relative ratio values normalized against healthy control for AR/STA vs. HC were calculated by the signal of AR/STA divided by the signal of HC. The fold changes (AR vs. HC or STA vs. HC) were then calculated based on these relative ratios. To determine the high (or low) expression abundance and up- (or down-) regulation in AR phenotype, two criteria were used: (a) Fold change of AR vs. HC was larger (or less) than 0 and (b) Fold change of AR vs. HC was larger (or less) than the fold change of STA vs. HC. Therefore, four groups of peptide signal intensity were categorized as (1) high abundance and up-regulation in AR, (2) low abundance and up-regulation in AR, (3) high abundance and down-regulation in AR, and (4) low abundance and down-regulation in AR. The box plots were drawn based on the fold changes in each group; in addition, the line graphs show that the signal intensity for each individual peptide either increased or decreased in AR vs. STA.
LC MALDI on Individual Samples to Verify Most Significant Peptide Biomarkers
We analyzed the 30 individual urine samples included in the first discovery phase along with ten individual urine samples from nonspecific proteinuric patients. The peptide samples for analysis were prepared and processed by the method, schematic of which is presented in Fig. 1.
Protein and Peptide Recovery
We previously established a standard protocol for urine collection and processing for urinary proteomics analysis . We followed the protocol to collect two separate fractions of small-MW endogenous peptides and large-MW proteins. Since our aim was to identify AR-specific endogenous peptides, the filtration method using a membrane with 10 kDa cutoff size served ideally.
When assayed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and linear mode MALDI-TOF, the filtrates were found to be smaller than 6 kDa molecular size (data not shown). The small-MW peptide fraction present in the filtrate was quantified by 2,4,6-trinitrobenzenesulfonic acid assay which is based on the measurement of primary amines and measuring the TNBS–primary amine conjugate . The mean peptide concentration in AR, STA, and HC categories was 156.5 ± 108.8, 344.6 ± 121.5, and 378.4 ± 130.1 μmol/dL, respectively. The mean protein concentration was 6.8 ± 3.8, 7.82 ± 2.2, and 5.5 ± 1.7 mg/dL in samples from AR, STA, and HC, respectively. The mean urine creatinine concentration was 59.1 ± 49.3, 104.4 ± 41.7, and 102.9 ± 38.2 mg/dL for AR, STA, and HC, respectively. Since proteinuric urine samples were not included in the study, there was no statistically significant difference in urine protein concentration among the three categories of samples.
LC MALDI Analysis of Small-MW Endogenous Peptides
We tested for the optimal amount of endogenous peptides to be fractionated for LC MALDI analysis. Results based on the mass spectrometric data suggested 3 nmol equivalents as the optimum amount (data not presented). Comparison of analysis by spotting direct to plate vs. LC MALDI showed large increase in number of features with the HPLC fractionation followed by MALDI MS analysis. The MS data consisted of a set of three sets of data points: the retention time dimension, the m/z dimension, and the intensity dimension. The “MASS-Conductor” software was used to transform the large volume of raw data into a list of nonredundant cross-category m/z features while simultaneously tracking associated sample source, retention time, and intensity. Figure 2 illustrates the biomarker discovery flow chart using Mass-Conductor data mining tools to process LC MS data sets from pooled samples of respective AR, STA, and HC categories. The analysis of ten repeated LC MALDI scan of the three pooled samples of classes AR, STA, and HC yielded 42.99 GB of raw data points (354,561,673 rows of records), 2.99 GB peak data points (6,295,689 rows of records), 528 MB monoisotopic feature (ion containing only the most abundant isotopes) data points (6,267,018 rows of records), and 10.52 MB unique monoisotopic feature data points across categories (106,760 rows of records) equivalent to 26,690 peptides.
List of peptides and their relative abundance in terms of fold change in AR urine when compared to STA urine with the ID of peptides that are sequenced
Swiss Prot ID
Increase in AR (n = 6)
Collagen alpha-1 (XI-chain)
Collagen alpha-3(V) chain
Decrease in AR (n = 5)
Increase in AR urine (n = 31)
Zn Finger Protein
Collagen alpha-3(V) chain
Collagen Alpha-1(I) chain
Collagen alpha-3(V) chain
Collagen alpha-3(V) chain
Vascular non-inflammatory molecule 2
Collagen alpha-3(V) chain
Albumin D box-binding protein
Collagen alpha-1 (V) chain
Collagen alpha-3(V) chain
Collagen alpha-1 (XVIII) chain
Collagen alpha-1 (XVIII) chain
Collagen alpha-1 (VIII) chain
Decrease in AR urine (n = 31)
Thyroid receptor-interacting protein 6
Collagen alpha-3 (V) chain
Collagen alpha-3 (V) chain
Cartilage intermediate lauer protein
Identification of Potential Biomarker Endogenous Peptides
Verification of Most Significant Candidate Peptides by LC MALDI on Individual Patients
Urinary peptides may provide much needed non-invasive biomarkers for early diagnosis of acute rejection of renal transplant. Unlike proteomics, where a smaller number (hundreds), of larger-MW proteins are assessed, peptidomics examines thousands of small-MW endogenous peptides in . Several top–down approaches have been used to analyze naturally occurring endogenous peptides. Currently, two preferred methods in peptidomics are CE MS  and LC MS [29–31]. Using CE MS method, Wittke et al. analyzed urine samples collected from renal transplant patients with AR, STA, and urinary tract infection and identified a distinct polypeptide pattern . LC-based, LC MS approach usually involves three main steps: (1) extraction of peptides, (2) fractionation of extracted peptides using HPLC, and (3) MS analysis of fractionated peptides for biomarker discovery purpose. Different strategies could be applied to fractionate the mixture of peptides. We used LC MALDI to identify potential biomarkers that could potentially be used as diagnostic surrogate biomarkers for acute kidney transplant rejection.
We have made several important findings in this study. Firstly, we have demonstrated that pooled strategy is a viable way to screen for potential biomarker peptides in urine. High throughput “omic” methods require a considerable amount of time per sample to be analyzed. There are conflicting opinions about pooled strategy. It is not advisable to pool samples wherever the aim is to identify very low abundance peptides because of the risk of losing the signal . However, pooling strategy helps in quickly screening for most significant candidates and proceeds further in the biomarker pathway with verification with individual samples.
In this effort to discover endogenous peptides that discriminate AR from stable graft, we had to address several confounding issues. Patient urine may have a variable peptide concentration, dependent on the individual’s meal, drink, and sleep patterns , which requires data to be normalized . In the absence of a consensus “housekeeping” peptide for normalization, we choose a strategy that was best available to us. To normalize total peptide used per analysis, we loaded equal amount (3 nmol) as quantified by TNBS assay. Another important factor is the ionization efficiency of the mass spectrometer employed for MS analysis. We used glu-fibrinopeptide as internal control for ionization efficiency and performed three MS scans of 2,000 laser shots per scan moving the laser every 50 shots.
The third important outcome of the study is that we hypothesized that AR-specific signature exists among endogenous urinary peptides. The results from our study showed that such peptides in fact exist (Table 2). The peptides could be classified in four distinct classes as shown in Fig. 3. Those four panels provided peptide candidate biomarkers that collectively distinguish urine from acute rejection patients from patients with stable graft function. We verified the trueness of the discovered peptide biomarkers resulted from the pooled approach using MALDI-TOF, by analyzing five most significant peptides on individual urine from ten AR patients and ten patients with stable graft function, including ten urine samples from nephrotic syndrome urine and ten urine collected from healthy normal controls. The successful verification of these peptides supported our pooled approach in initial screening of biomarkers.
Yet another achievement of this study is that we have identified 54 peptide fragments among 73 listed in Table 2. Even though identification endogenous peptides is more difficult compared to proteolytically cleaved peptides such as trypsin digested peptides, we identified several endogenous peptides which belong to either proteins of either renal origin or related with kidney dysfunction. Among the proteins identified include Tamm–Horsfall protein (UMOD), the most abundant protein in human urine; β-2 microglobulin (B2M), a cleaved product as well as the intact protein which has been reported as potential biomarker protein for AR by two independent groups [13, 35]; kininogen (KNG1), reported to be related to pathophysiology of hypertension and renal diseases ; and prostaglandin-H2 D-isomerase is reported to be expressed in kidney tubules (Human Protein Atlas—http://proteinatlas.org).
Finally, a number of peptide fragments of Tamm–Horsfall protein were observed to be significantly lower in AR urine when compared to STA urine and the urine collected from healthy normal controls. Trueness of this finding has been verified by analyzing individual samples. This observation of peptide fragments from other kidney-specific proteins may be an indication of a possible role of protease and protease inhibitor activities at the time of acute rejection. In an ongoing gene-expression analysis of biopsies of AR and STA patients, we have observed significantly low expression of UMOD gene (P = 0.008) in a total of 64 biopsy microarrays that included 19 AR and 45 non-AR biopsy samples (Sarwal et al. 2008, unpublished data). This observation of a consistent low expression of UMOD at the transcript level as well its peptides may help us achieve a better insight on possible events associated with AR and even to investigate THP, physiological role of which has intrigued many researchers.
The observation of altered concentration of THP peptides in acute rejection vs stable graft will have to be investigated further with specific focus on the role of proteases and protease inhibitor activities. One of the ways to study such activity is to look for their cleavage pattern to see if they indicate activation of any specific protease/s. In a published report, Villanueva et al. identified a signature subset of serum peptides for three types of solid tumors but also to link peptide marker profiles for disease conditions directly to differential protease activity . Such study in case of urinary peptides is possible with a larger patient cohort and with appropriate in vitro assays which is out of scope for this focused report on screening for potential biomarkers.
The important clinical utility aspect of this study is that the identified potential biomarker peptides will be verified in subsequent verification step using quantitative approach such as Multiple Reaction Monitoring (MRM) or enzyme-linked immunosorbent assays. Such quantitative analysis on a larger cohort of independent samples will help shorten the list of biomarkers which then could be taken to clinical trial.
In summary, for the first time, we have shown that LC MALDI is a useful tool to screen for potential non-invasive urinary peptide biomarkers for acute rejection. We identified a set of peptides as potential biomarkers for AR. We tested the trueness of the discovery on five of the most significant peptide candidates and demonstrated that LC MALDI on pooled urine samples for discovery is a reliable strategy for screening phase of biomarker discovery. A verification study is now necessary to further the outcome of this study, which is underway with more patients and disease categories included.
Stable graft function
Healthy normal control
Liquid chromatography followed by matrix-assisted laser desorption/ionization
The work was supported by NIH Grant RO1-AI-061739, awarded to MS, and Deans Fellowship and Child Health Research Program Fellowship to TS. We thank Tonya Pekar and members of the Sarwal Lab for their help in the preparation of the manuscript.
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