Proteomics and Metabolomics as Tools to Unravel Novel Culprits and Mechanisms of Uremic Toxicity: Instrument or Hype?

The membrane perspective of uraemic toxins: which ones should, or can, be removed?

Informed decision-making is paramount to the improvement of dialysis therapies and patient outcomes. A cornerstone of delivery of optimal dialysis therapy is to delineate which substances (uraemic retention solutes or 'uraemic toxins') contribute to the condition of uraemia in terms of deleterious biochemical effects they may exert. Thereafter, decisions can be made as to which of the accumulated compounds need to be targeted for removal and by which strategies. For haemodialysis (HD), the non-selectivity of membranes is sometimes considered a limitation. Yet, considering that dozens of substances with potential toxicity need to be eliminated, and targeting removal of individual toxins explicitly is not recommended, current dialysis membranes enable elimination of several molecules of a broad size range within a single therapy session. However, because HD solute removal is based on size-exclusion principles, i.e. the size of the substances to be removed relative to the mean size of the 'pores' of the membrane, only a limited degree of selectivity of removal is possible. Removal of unwanted substances during HD needs to be weighed against the unavoidable loss of substances that are recognized to be necessary for bodily functions and physiology. In striving to improve the efficiency of HD by increasing the porosity of membranes, there is a greater potential for the loss of substances that are of benefit. Based on this elementary trade-off and availability of recent guidance on the relative toxicity of substances retained in uraemia, we propose a new evidence-linked uraemic toxin elimination (ELUTE) approach whereby only those clusters of substances for which there is a sufficient body of evidence linking them to deleterious biological effects need to be targeted for removal. Our approach involves correlating the physical properties of retention solutes (deemed to express toxicity) with key determinants of membranes and separation processes. Our analysis revealed that in attempting to remove the relatively small number of 'larger' substances graded as having only moderate toxicity, uncontrolled (and efficient) removal of several useful compounds would take place simultaneously and may compromise the well-being or outcomes of patients. The bulk of the uraemic toxin load comprises uraemic toxins below <30 000 Da and are adequately removed by standard membranes. Further, removal of a few difficult-to-remove-by-dialysis (protein-bound) compounds that express toxicity cannot be achieved by manipulation of pore size alone. The trade-off between the benefits of effective removal of the bulk of the uraemic toxin load and risks (increased loss of useful substances) associated with targeting the removal of a few larger substances in 'high-efficiency' HD treatment strategies needs to be recognized and better understood. The removability during HD of substances, be they toxic, inert or beneficial, needs be revised to establish the pros and cons of current dialytic elimination strategies.  .

A Systems-Level View of Renal Metabolomics

The measurement of select circulating metabolites such as creatinine, glucose, and cholesterol are integral to clinical medicine, with implications for diagnosis, prognosis, and treatment. Metabolomics studies in nephrology research seek to build on this paradigm, with the goal to identify novel markers and causal participants in the pathogenesis of kidney disease and its complications. This article reviews three themes pertinent to this goal. Each is rooted in long-established principles of human physiology, with recent updates enabled by metabolomics and other tools. First, the kidney has a broad and heterogeneous impact on circulating metabolites, with progressive loss of kidney function resulting in a multitude of small molecule alterations. Second, an increasing number of circulating metabolites have been shown to possess functional roles, in some cases acting as ligands for specific G-protein-coupled receptors. Third, circulating metabolites traffic through varied, and sometimes complex, interorgan circuits. Taken together, these themes emphasize the importance of viewing renal metabolomics at the systems level, recognizing the diverse origins and physiologic effects of blood metabolites. However, how to synthesize these themes and how to establish clinical relevance remain uncertain and will require further investigation.

Targeted Metabolomic Profiling of Peritoneal Dialysis Effluents Shows Anti-oxidative Capacity of Alanyl-Glutamine

Readily available peritoneal dialysis (PD) effluents from PD patients in the course of renal replacement therapy are a potentially rich source for molecular markers for predicting clinical outcome, monitoring the therapy, and therapeutic interventions. The complex clinical phenotype of PD patients might be reflected in the PD effluent metabolome. Metabolomic analysis of PD effluent might allow quantitative detection and assessment of candidate PD biomarkers for prognostication and therapeutic monitoring. We therefore subjected peritoneal equilibration test effluents from 20 stable PD patients, obtained in a randomized controlled trial (RCT) to evaluate cytoprotective effects of standard PD solution (3.86% glucose) supplemented with 8 mM alanyl-glutamine (AlaGln) to targeted metabolomics analysis. One hundred eighty eight pre-defined metabolites, including free amino acids, acylcarnitines, and glycerophospholipids, as well as custom metabolic indicators calculated from these metabolites were surveyed in a high-throughput assay requiring only 10 μl of PD effluent. Metabolite profiles of effluents from the cross-over trial were analyzed with respect to AlaGln status and clinical parameters such as duration of PD therapy and history of previous episodes of peritonitis. This targeted approach detected and quantified 184 small molecules in PD effluent, a larger number of detected metabolites than in all previous metabolomic studies in PD effluent combined. Metabolites were clustered within substance classes regarding concentrations after a 4-h dwell. PD effluent metabolic profiles were differentiated according to PD patient sub-populations, revealing novel changes in small molecule abundance during PD therapy. AlaGln supplementation of PD fluid altered levels of specific metabolites, including increases in alanine and glutamine but not glutamate, and reduced levels of small molecule indicators of oxidative stress, such as methionine sulfoxide. Our study represents the first application of targeted metabolomics to PD effluents. The observed metabolomic changes in PD effluent associated with AlaGln-supplementation during therapy suggested an anti-oxidant effect, and were consistent with the restoration of important stress and immune processes previously noted in the RCT. High-throughput detection of PD effluent metabolomic signatures and their alterations by therapeutic interventions offers new opportunities for metabolome-clinical correlation in PD and for prescription of personalized PD therapy.

Personalized Approach and Precision Medicine in Supportive and End-of-Life Care for Patients With Advanced and End-Stage Kidney Disease

Kidney supportive care requires a highly personalized approach to care. Precision medicine holds promise for a deeper understanding of the pathophysiology of symptoms and related syndromes and more precise individualization of prognosis and treatment estimates, therefore providing valuable opportunities for greater personalization of supportive care. However, the major drivers of quality of life are psychosocial, economic, lifestyle, and preference-based, and consideration of these factors and skilled communication are integral to the provision of excellent and personalized kidney supportive care. This article discusses the concepts of personalized and precision medicine in the context of kidney supportive care and highlights some opportunities and limitations within these fields.

Examining hemodialyzer membrane performance using proteomic technologies

The success and the quality of hemodialysis therapy are mainly related to both clearance and biocompatibility properties of the artificial membrane packed in the hemodialyzer. Performance of a membrane is strongly influenced by its interaction with the plasma protein repertoire during the extracorporeal procedure. Recognition that a number of medium-high molecular weight solutes, including proteins and protein-bound molecules, are potentially toxic has prompted the development of more permeable membranes. Such membrane engineering, however, may cause loss of vital proteins, with membrane removal being nonspecific. In addition, plasma proteins can be adsorbed onto the membrane surface upon blood contact during dialysis. Adsorption can contribute to the removal of toxic compounds and governs the biocompatibility of a membrane, since surface-adsorbed proteins may trigger a variety of biologic blood pathways with pathophysiologic consequences. Over the last years, use of proteomic approaches has allowed polypeptide spectrum involved in the process of hemodialysis, a key issue previously hampered by lack of suitable technology, to be assessed in an unbiased manner and in its full complexity. Proteomics has been successfully applied to identify and quantify proteins in complex mixtures such as dialysis outflow fluid and fluid desorbed from dialysis membrane containing adsorbed proteins. The identified proteins can also be characterized by their involvement in metabolic and signaling pathways, molecular networks, and biologic processes through application of bioinformatics tools. Proteomics may thus provide an actual functional definition as to the effect of a membrane material on plasma proteins during hemodialysis. Here, we review the results of proteomic studies on the performance of hemodialysis membranes, as evaluated in terms of solute removal efficiency and blood-membrane interactions. The evidence collected indicates that the information provided by proteomic investigations yields improved molecular and functional knowledge and may lead to the development of more efficient membranes for the potential benefit of the patient.

Co-Expression Analysis of Blood Cell Genome Expression to Preliminary Investigation of Regulatory Mechanisms in Uremia

Background

Uremia involves a series of clinical manifestations and is a common syndrome that occurs in nearly all end-stage kidney diseases. However, the exact genetic and/or molecular mechanisms that underlie uremia remain poorly understood.

Material/Methods

In this case-control study, we analyzed whole-genome microarray of 75 uremia patients and 20 healthy controls to investigate changes in gene expression and cellular mechanisms relevant to uremia. Gene co-expression network analysis was performed to construct co-expression networks using differentially expressed genes (DEGs) in uremia. We then determined hub models of co-expressed gene networks by MCODE, and we used miRNA enrichment analysis to detect key miRNAs in each hub module.

Results

We found nine co-expressed hub modules implicated in uremia. These modules were enriched in specific biological functions, including “proteolysis”, “membrane-enclosed lumen”, and “apoptosis”. Finally, miRNA enrichment analysis to detect key miRNAs in each hub module found 15 miRNAs that were specifically targeted to uremia-related hub modules. Of these, miRNA-21-3p and miRNA-210-3p have been identified in other studies as being important for uremia.

Conclusions

In summary, our study connected biological functions, genes, and miRNAs that underpin the network modules that can be used to elucidate the molecular mechanisms involved in uremia.

Uraemic toxins and new methods to control their accumulation: game changers for the concept of dialysis adequacy

The current concept of an adequate dialysis based only on the dialysis process itself is rather limited. We now have considerable knowledge of uraemic toxicity and improved tools for limiting uraemic toxin accumulation. It is time to make use of these. A broader concept of adequacy that focusses on uraemic toxicity is required. As discussed in the present review, adequacy could be achieved by many different methods in combination with, or instead of, dialysis. These include preservation of renal function, dietary intake, reducing uraemic toxin generation rate and intestinal absorption, isolated ultrafiltration and extracorporeal adsorption of key uraemic toxins. A better measure of the quality of dialysis treatment would quantify the uraemic state in the patient using levels of a panel of key uraemic toxins. Treatment would focus on controlling uraemic toxicity while reducing harm or inconvenience to the patient. Delivering more dialysis might not be the best way to achieve this.

New methods and technologies for measuring uremic toxins and quantifying dialysis adequacy

This publication reviews the currently available methods to identify uremic retention solutes, to determine their biological relevance and to quantify their removal. The analytical methods for the detection of uremic solutes have improved continuously, allowing the identification of several previously unknown solutes. Progress has been accelerated by the development of comprehensive strategies such as genomics, proteomics and the latest "omics" area, metabolomics. Those methodologies will be further refined in future. Once the concentration of solutes of interest is known based on targeted analysis, their biological relevance can be studied by means of in vitro, ex vivo, or animal models, provided those are representative for the key complications of the uremic syndrome. For this to come to pass, rigid protocols should be applied, e.g., aiming at free solute concentrations conform those found in uremia. Subsequently, the decrease in concentration of relevant solutes should be pursued by nondialysis (e.g., by influencing nutritional intake or intestinal generation, using sorbents, modifying metabolism, or preserving renal function) and dialysis methods. Optimal dialysis strategies can be sought by studying solute kinetics during dialysis. Clinical studies are necessary to assess the correct impact of those optimized strategies on outcomes. Although longitudinal studies of solute concentration and surrogate outcome studies are first steps in suggesting the usefulness of a given approach, ultimately hard outcome randomized controlled trials are needed to endorse evidence-based therapeutic choices. The nonspecificity of dialysis removal is however a handicap limiting the chances to provide proof of concept that a given solute or group of solutes has definite biological impact.

Protein-bound molecules: a large family with a bad character

Many small solutes excreted by the kidney are bound to plasma proteins, chiefly albumin, in the circulation. The combination of protein binding and tubular secretion allows the kidney to reduce the free, unbound concentrations of such solutes to lower levels than could be obtained by tubular secretion alone. Protein-bound solutes accumulate in the plasma when the kidneys fail, and the free, unbound levels of these solutes increase more than their total plasma levels owing to competition for binding sites on plasma proteins. Given the efficiency by which the kidney can clear protein-bound solutes, it is tempting to speculate that some compounds in this class are important uremic toxins. Studies to date have focused largely on two specific protein-bound solutes: indoxyl sulfate and p-cresyl sulfate. The largest body of evidence suggests that both of these compounds contribute to cardiovascular disease, and that indoxyl sulfate contributes to the progression of chronic kidney disease. Other protein-bound solutes have been investigated to a much lesser extent, and could in the future prove to be even more important uremic toxins.