Markedly Increased Urinary Preprohaptoglobin and Haptoglobin in Passive Heymann Nephritis: A Differential Proteomics Approach

Progress in understanding primary glomerular disease: insights from urinary proteomics and in-depth analyses of potential biomarkers based on bioinformatics

Chronic kidney disease (CKD) has become a global public health challenge. While primary glomerular disease (PGD) is one of the leading causes of CKD, the specific pathogenesis of PGD is still unclear. Accurate diagnosis relies largely on invasive renal biopsy, which carries risks of bleeding, pain, infection and kidney vein thrombosis. Problems with the biopsy procedure include lack of glomeruli in the tissue obtained, and the sampling site not being reflective of the overall lesion in the kidney. Repeated renal biopsies to monitor disease progression cannot be performed because of the significant risks of bleeding and kidney vein thrombosis. On the other hand, urine collection, a noninvasive method, can be performed repeatedly, and urinary proteins can reflect pathological changes in the urinary system. Advancements in proteomics technologies, especially mass spectrometry, have facilitated the identification of candidate biomarkers in different pathological types of PGD. Such biomarkers not only provide insights into the pathogenesis of PGD but also are important for diagnosis, monitoring treatment, and prognosis. In this review, we summarize the findings from studies that have used urinary proteomics, among other omics screens, to identify potential biomarkers for different types of PGD. Moreover, we performed an in-depth bioinformatic analysis to gain a deeper understanding of the biological processes and protein-protein interaction networks in which these candidate biomarkers may participate. This review, including a description of an integrated analysis method, is intended to provide insights into the pathogenesis, noninvasive diagnosis, and personalized treatment efforts of PGD and other associated diseases.

Urinary proteome of dogs with renal disease secondary to leishmaniosis

Canine leishmaniosis is frequently associated with the development of renal disease. Its pathogenesis is complex and not fully understood. For this reason, this study aimed to describe the urinary proteome, and identify possible new biomarkers in dogs with kidney disease secondary to leishmaniosis. Urine samples were collected from 20 dogs, 5 from healthy dogs, and 15 from stages Leishvet III and IV. Urine samples were analyzed by UHPLC-MS/MS. The data are available via ProteomeXchange with identifier PXD029165. A total of 951 proteins were obtained. After bioinformatic analysis, 93 urinary proteins were altered in the study group. Enrichment analysis performed on these proteins showed an overrepresentation of the complement activation pathway, among others. Finally, 12 discriminant variables were found in dogs with renal disease secondary to leishmaniosis, highlighting C4a anaphylatoxin, apolipoprotein A-I, haptoglobin, leucine-rich alpha-2-glycoprotein 1, and beta-2-microglobulin. This study is the first to describe the urinary proteomics of dogs with renal disease caused by leishmaniosis, and it provides new possible biomarkers for the diagnosis and monitoring of this disease.

Effects of arginine vasopressin on the urine proteome in rats

Biomarkers are the measurable changes associated with a physiological or pathophysiological process. The content of urine frequently changes because it is not controlled by homeostatic mechanisms, and these alterations can be a source of biomarkers. However, urine is affected by many factors. In this study, vasoconstrictor and antidiuretic arginine vasopressin (AVP) were infused into rats using an osmotic pump. The rats’ urinary proteome after one week of infusion was analyzed by label-free LC-MS/MS. A total of 408 proteins were identified; among these proteins, eight and 10 proteins had significantly altered expression in the low and high dose groups, respectively, compared with the control group using the one-way ANOVA analysis followed by post hoc analysis with the least significant difference (LSD) test or Dunnett’s T3 test. Three differential proteins were described in prior studies as related to AVP physiological processes, and nine differential proteins are known disease biomarkers. Sixteen of the 17 differential proteins have human orthologs. These results suggest that we should consider the effects of AVP on urinary proteins in future urinary disease biomarker researches. The study data provide clues regarding underlying mechanisms associated with AVP for future physiological researches on AVP. This study provide a sensitive changes associated with AVP. However, the limitation of this result is that the candidate biomarkers should be further verified and filtered. Large clinical samples must be examined to verify the differential proteins identified in this study before these proteins are used as biomarkers for pathological AVP increased diseases, such as syndrome of inappropriate antidiuretic hormone secretion (SIADH).

Urine protein concentration estimation for biomarker discovery

Recent advances have been made in the study of urinary proteomics as a diagnostic tool for renal disease and pre-eclampsia which requires accurate measurement of urinary protein. We compared different protein assays (Bicinchoninic acid (BCA), Lowry and Bradford) against the 'gold standard' amino-acid assay in urine from 43 women (8 non-pregnant, 34 pregnant, including 8 with pre-eclampsia). BCA assay was superior to both Lowry and Bradford assays (Bland Altman bias: 0.08) compared to amino-acid assay, which performed particularly poorly at higher protein concentrations. These data highlight the need to use amino-acid or BCA assays for unprocessed urine protein estimation.

Proteomic identification network analysis of haptoglobin as a key regulator associated with liver fibrosis

Liver fibrosis (LF) is the final stage of liver dysfunction, characterized by diffuse fibrosis which is the main response to the liver injury. Haptoglobin (HP) protein, produced as an acute phase reactant during LF, preventing liver damage, may be potential molecular targets for early LF diagnostics and therapeutic applications. However, protein networks associated with the HP are largely unknown. To address this issue, we used a pathological mouse model of LF that was induced by treatment with carbon tetrachloride for 8 days. HP protein was separated and identified by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. HP protein was subjected to functional pathway analysis using STRING and Cytoscape software for better understanding of the protein-protein interaction (PPI) networks in biological context. Bioinformatics analyses revealed that HP expression associated with fibrosis was upregulated, and suggested that HP responsible for fibrosis may precede the onset and progression of LF. Using the web-based database, functional pathway analysis suggested the modulation of multiple vital physiological pathways, including antioxidation immunity, signal transduction, metabolic process, energy production, cell apoptosis, oxidation reduction, DNA repair process, cell communication, and regulation of cellular process. The generation of protein interaction networks clearly enhances the interpretation and understanding of the molecular mechanisms of HP. HP protein represents targets for further experimental investigation that will provide biological insight and potentially could be exploited for novel therapeutic approaches to combat LF.

Redox proteomics in study of kidney-associated hypertension: new insights to old diseases

SIGNIFICANCE

The kidney helps to maintain low blood pressure in the human body, and impaired kidney function is a common attribute of aging that is often associated with high blood pressure (hypertension). Kidney-related pathologies are important contributors (either directly or indirectly) to overall human mortality. In comparison with other organs, kidney has an unusually wide range of oxidative status, ranging from the well-perfused cortex to near-anoxic medulla.

RECENT ADVANCES

Oxidative stress has been implicated in many kidney pathologies, especially chronic kidney disease, and there is considerable research interest in oxidative stress biomarkers for earlier prediction of disease onset. Proteomics approaches have been taken to study of human kidney tissue, serum/plasma, urine, and animal models of hypertension.

CRITICAL ISSUES

Redox proteomics, in which oxidative post-translational modifications can be identified in protein targets of oxidative or nitrosative stress, has not been very extensively pursued in this set of pathologies.

FUTURE DIRECTIONS

Proteomics studies of kidney and related tissues have relevance to chronic kidney disease, and redox proteomics, in particular, represents an under-exploited toolkit for identification of novel biomarkers in this commonly occurring pathology.

Proteomics-based investigations of animal models of disease

Cells contain a large yet, constant genome, which contains all the coding information necessary to sustain cellular physiology. However, proteins are the end products of genes, and hence dictate the phenotype of cells and tissues. Therefore, proteomics can provide key information for the elucidation of physiological and pathophysiological mechanisms by identifying the protein profile from cells and tissues. The relatively novel techniques used for the study of proteomics thus have the potential to improve diagnostic, prognostic, as well as therapeutic avenues. In this review, we first discuss the benefits of animal models over the use of human samples for the proteomic analysis of human disease. Next, we aim to demonstrate the potential of proteomics in the elucidation of disease mechanisms that may not be possible by other conventional technologies. Following this, we describe the use of proteomics for the analysis of PTM and protein interactions in animal models and their relevance to the study of human disease. Finally, we discuss the development of clinical biomarkers for the early diagnosis of disease via proteomic analysis of animal models. We also discuss the development of standard proteomes and relate how this data will benefit future proteomic research. A comprehensive review of all animal models used in conjunction with proteomics is beyond the scope of this manuscript. Therefore, we aimed to cover a large breadth of topics, which together, demonstrate the potential of proteomics as a powerful tool in biomedical research.

Proteomic analysis of changes in protein expression in serum from animals exposed to paraquat

Paraquat (PQ) poisoning remains a major public health concern in many countries. Extensive research has focused on finding early diagnostic biomarkers of acute PQ poisoning. In order to investigate the characterization of diagnostic biomarkers in PQ poisoning, we utilized proteomic analysis using serum from rats exposed to PQ, and we identified 8 differentially expressed proteins from over 500 protein spots. The expression of apolipoprotein E (ApoE), preprohaptoglobin (Pphg), a precursor of haptoglobin (Hp), and complement component 3 (C3) proteins was greatly induced by PQ exposure while the expression of fibrinogen γ-chain (FGG) and Ac-158 was dramatically reduced. To further investigate the possibility of ApoE, Pphg and FGG as useful diagnostic biomarkers of PQ poisoning, western blot and qRT-PCR analyses were conducted using cell lines as well as rat and human sera. The expression levels of ApoE, Hp and FGG were significantly altered in the presence of PQ in both rat and human serum suggesting that these proteins may be appropriate candidate molecular biomarkers for the early diagnosis of acute PQ intoxication.

Differential proteome profiling using iTRAQ in microalbuminuric and normoalbuminuric type 2 diabetic patients

Diabetic nephropathy (DN) is a long-term complication of diabetes mellitus that leads to end-stage renal disease. Microalbuminuria is used for the early detection of diabetic renal damage, but such levels do not reflect the state of incipient DN precisely in type 2 diabetic patients because microalbuminuria develops in other diseases, necessitating more accurate biomarkers that detect incipient DN. Isobaric tags for relative and absolute quantification (iTRAQ) were used to identify urinary proteins that were differentially excreted in normoalbuminuric and microalbuminuric patients with type 2 diabetes where 710 and 196 proteins were identified and quantified, respectively. Some candidates were confirmed by 2-DE analysis, or validated by Western blot and multiple reaction monitoring (MRM). Specifically, some differentially expressed proteins were verified by MRM in urine from normoalbuminuric and microalbuminuric patients with type 2 diabetes, wherein alpha-1-antitrypsin, alpha-1-acid glycoprotein 1, and prostate stem cell antigen had excellent AUC values (0.849, 0.873, and 0.825, resp.). Moreover, we performed a multiplex assay using these biomarker candidates, resulting in a merged AUC value of 0.921. Although the differentially expressed proteins in this iTRAQ study require further validation in larger and categorized sample groups, they constitute baseline data on preliminary biomarker candidates that can be used to discover novel biomarkers for incipient DN.

Proteomic profiling identifies haptoglobin as a potential serum biomarker for steroid-resistant nephrotic syndrome

BACKGROUND

Long-term outcomes for patients with adult idiopathic nephrotic syndrome correlate closely with steroid responsiveness. The aim of this prospective study was to evaluate the difference in serum proteomes between steroid-sensitive nephrotic syndrome (SSNS) and steroid-resistant nephrotic syndrome (SRNS) patients and identify potential biomarkers for the prediction of SRNS.

METHODS

We performed a gel-based proteomic study of serum obtained from SRNS and SSNS patients and healthy controls at the time of presentation (n = 6 for each group). Proteins from the serum samples were separated using 2-D electrophoresis, digested in-gel and subjected to MALDI-TOF-MS/MS analysis. Further validation was performed utilizing Western blot and ELISA. The sensitivities and specificities of the candidate proteins for predicting SRNS were determined using receiver operating characteristic curves.

RESULTS

Thirteen differentially expressed proteins were identified as haptoglobin (Hp) with different isoelectric points and molecular weights. Western blot and ELISA analysis of samples from 146 subjects (healthy controls = 52, SSNS = 54, SRNS = 40) showed a markedly increased level of Hp in the serum, but not urine, of SRNS compared to SSNS patients. The optimal serum cutoff level of Hp was set at ≥1,279 µg/ml using the receiver operating characteristic curve. The sensitivity and specificity for predicting SRNS were 85.0 and 96.3%, respectively.

CONCLUSIONS

This study provides a novel overview of the difference in serum proteomes of SSNS and SRNS patients. Serum Hp may be a useful predictive biomarker for steroid therapy efficacy in the treatment of idiopathic nephrotic syndrome.

Proteomic analysis of post-hemorrhagic shock mesenteric lymph

Recent studies have documented the association of mesenteric lymphatic route with adult respiratory distress syndrome and multiple organ failure after hemorrhagic shock. However, the mediators and mechanisms of the toxic effects of mesenteric lymph remain unclear. This study aimed to identify mediators or biomarkers in the mesenteric lymph through comparative proteomic analysis. Fourteen mature male Sprague-Dawley rats were randomly divided and subjected to trauma (laparotomy) plus hemorrhagic shock or trauma plus sham shock. Mesenteric lymph samples were collected before shock and at 3 h after resuscitation from hemorrhagic shock (or sham shock). To investigate changes in proteome profiles between preshock and 3-h postshock (or 3-h post-sham shock) mesenteric lymph samples, two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry were performed. We found a more than 2-fold change in abundance of 31 protein spots in the lymph samples. Mass spectrometry analyses identified 12 distinct proteins. Four proteins were consistently upregulated in the 3-h postshock lymph samples, including serum albumin precursor, two isoforms of cytoplasmic actin, complement C3 precursor, and major urinary protein precursor. Two proteins, including haptoglobin and one unidentified protein, were consistently downregulated. The deregulation of these proteins was confirmed by Western blots. Most of these altered proteins are functionally implicated in tissue inflammation. The findings of this study provide a starting point for investigating the functions of these proteins in hemorrhagic shock-induced lung injury and hold great promise for the development of potential therapeutic interventions.

Urinary proteomics--a tool for biomarker discovery

The strong need for the discovery of novel disease markers together with the development of high-throughput techniques that provide highly sensitive analysis of protein content in tissues and bodily fluids, using proteomics, has opened the completely new chapter in biomarker discovery. The detection of biomarkers based on urinary proteome analysis is rapidly advancing and may provide new tools to improve non-invasive diagnostics, prognostics, and therapy enhancement. As a tool for biomarker discovery, urinary proteomics is especially fruitful in the area of early diagnostics and differentiation of renal damage, and it possesses enormous potential for improving and expanding non-invasive cancer diagnostics. An abundance of urinary proteins could provide a wide variety of biomarkers for the diagnosis and follow-up of many systemic diseases as well. This article reviews the utility of urinary proteomics for biomarker discovery from the perspective of clinical application. Despite huge potential and prompt development of urinary proteomics, many challenges are still in front of us. Research effort and financial investment have to be oriented on providing strategies for exceeding current methodological and technical obstacles in a way to ensure the successful validation and implementation of newly discovered urinary biomarkers. The result is expected to be the development of new non-invasive tests and procedures able to guarantee higher efficiency of patient care and provide needed personalized medical approach.

Two-dimensional difference gel electrophoresis urinary proteomic profile in the search of nonimmune chronic allograft dysfunction biomarkers

INTRODUCTION

Despite advances in therapeutics, graft loss associated with chronic allograft dysfunction (CAD) remains high. Urinary proteomic analysis is a noninvasive method that could be used to detect and evaluate CAD in renal transplant recipients. This study was aimed to establish the normal proteome map of stable transplant patients and to validate the utility of two-dimensional difference gel electrophoresis (2DE-DIGE) in identifying new candidates as urinary biomarkers of CAD.

METHODS

Morning spot urine samples that were collected from kidney transplant recipients with biopsy-proven interstitial fibrosis and tubular atrophy (IFTA) stages 0-I-II/III (n=8/group) under immunosuppressive treatment with tacrolimus plus mycophenolate with or without prednisone. 2DE silver staining and mass spectrometry analyses were used to establish the normal proteome map, and 2DE-DIGE and mass spectrometry were used to identify proteins exhibiting differential abundance.

RESULTS AND CONCLUSIONS

This study defines the normal proteome of stable renal transplant patients, which is composed of several plasma proteins, as well as of immunologic proteins that are probably specific to transplant recipients. The 2DE-DIGE study showed 19 proteins with differential concentrations, depending on the IFTA histologic score. These 19 proteins could be used as urinary biomarkers of the severity of IFTA in renal transplant recipients.

Congenital disorder of glycosylation Ia: new differentially expressed proteins identified by 2-DE

Congenital disorders of glycosylation (CDG) comprise a family of inherited multisystemic disorders resulting from the deficiency of glycosylation pathways. N-glycosylation defects are classified as two biochemical and genetic established types, of which CDG-Ia is the most frequent. We performed 2-DE proteomic analysis on serum from two functional hemizygous CDG-Ia patients bearing T237M and D65Y missense changes. Comparative analysis of control/patient serum proteome allowed us to identify differential expression of 14 proteins. The most remarkable groups included proteins involved in immune response, coagulation mechanism and tissue protection against oxidative stress. The patient bearing D65Y mutation had less favourable clinical outcome and showed more abnormalities in the spot patterns, suggesting that the proteomic results might also be correlated with the phenotype of CDG patients. This study describes for the first time the differential expression of alpha(2)-macroglobulin, afamin, fibrin and fibrinogen in CDG disorder and shows how the proteomic approach might be useful for understanding its physiopathology.

Differential ConA-enriched urinary proteome in rat experimental glomerular diseases

Glomerular diseases are leading causes of end-stage renal diseases worldwide. They are considered to be consequences of injury primarily to the three types of glomerular cells. Differential diagnosis typically relies on invasive biopsy findings. We expected that injuries of different glomerular cells would cause different changes in urinary proteome. The goal of this study was to identify differential urinary proteins distinguishing between injuries of different glomerular cells before significant histopathologic changes. Adriamycin nephropathy and Thy1.1 glomerulonephritis were employed as models with different primary impaired cells. ConA-enriched urinary glycoproteome on day3 were profiled by gel-free shotgun tandem mass spectrometry, and compared with self-healthy controls to identify differential urinary proteins for each model. By comparing the changes of the differential proteins between these two models, we identified 39 proteins with different directions of changes, which may potentially be useful in differentiation; and 7 proteins with the same direction of changes, which may be potential indicators of early renal damage. These differential proteins were of several origins: plasma proteins, proteins with urine or kidney specificity, proteins without tissue-specificity (mainly inflammatory mediators) etc. Our results may help better understand the effects of injuries of different glomerular cells at the initial stage, and lead to the discovery of novel early diagnostic markers for human focal segmental glomerulosclerosis (FSGS) and mesangioproliferative glomerulonephritis (MsPGN) which have the same primary impaired cells with adriamycin nephropathy and Thy1.1 glomerulonephritis, respectively.

Body fluid proteomics for biomarker discovery: lessons from the past hold the key to success in the future

Sparked by the article from Lescuyer and colleagues in a recent issue, we aim here to further encourage interest in and discussion of clinically relevant biomarker research. We express our view on proteomics for biomarker discovery by addressing multiple relevant issues, including the inherent differences between biological fluids (and how these differences affect current analytical approaches) and experimental design to maximize the efficiency of moving from the bench to the bedside. Herein, we also include suggestions for definition of the term "biomarker", based on the use of a set of universal characterization/validation requirements, and illustrate several recent examples of successful transitions of benchtop proteomic studies work to clinical practice.