Proteomic analysis of acute kidney injury: biomarkers to mechanisms

Monitoring the fluctuation of hydrogen peroxide with a near-infrared fluorescent probe for the diagnosis and management of kidney injury

Kidney injury has become an increasing concern for patients because of environmental hazards and physiological factors. However, the early diagnosis of kidney injury remains challenging. Studies have shown that oxidative stress was closely related to the occurrence and development of kidney injury, in which abnormal hydrogen peroxide (H2O2) production was a common characteristic. Consequently, monitoring H2O2 level changes is essential for the diagnosis and management of kidney injury. Herein, based on fluorescence imaging advantages, a near-infrared fluorescent probe DHX-1 was designed to detect H2O2. DHX-1 showed high sensitivity and selectivity toward H2O2, with a fast response time and excellent imaging capacity for H2O2 in living cells and zebrafish. DHX-1 could detect H2O2 in pesticide-induced HK-2 cells, revealing the main cause of kidney injury caused by pesticides. Moreover, we performed fluorescence imaging, which confirmed H2O2 fluctuation in kidney injury caused by uric acid. In addition, DHX-1 achieved rapid screening of active compounds to ameliorate pesticide-induced kidney injury. This study presents a tool and strategy for monitoring H2O2 levels that could be employed for the early diagnosis and effective management of kidney injury.

Discovering a New Drug Against Acute Kidney Injury by Using a Tailored Photoacoustic Imaging Probe

Acute kidney injury (AKI) has become an increasing concern for patients due to the widespread clinical use of nephrotoxic drugs. Currently, the early diagnosis of AKI is still challenging and the available therapeutic drugs cannot meet the clinical demand. Herein, this work has investigated the key redox couple involved in AKI and develops a tailored photoacoustic (PA) imaging probe (AB-DiOH) which can reversibly respond to hypochlorite (ClO-)/glutathione (GSH) with high specificity and sensitivity. This probe enables the real-time monitoring of AKI by noninvasive PA imaging, with better detection sensitivity than the blood test. Furthermore, this probe is utilized for screening nephroprotective drugs among natural products. For the first time, astragalin is discovered to be a potential new drug for the treatment of AKI. After oral administration, astragalin can be efficiently absorbed by the animal body, alleviate kidney injury, and meanwhile induce no damage to other normal tissues. The treatment mechanism of astragalin has also been revealed to be the simultaneous inhibition of oxidative stress, ferroptosis, and cuproposis. The developed PA imaging probe and the discovered drug candidate provide a promising new tool and strategy for the early diagnosis and effective treatment of AKI.

Evaluation of Renal Function with Urinary NGAL and Doppler Ultrasonography in ICU Patients: A 1-Year Observational Pilot Study

BACKGROUND

We estimated the diagnostic accuracy of urinary NGAL for the diagnosis of AKI.

METHODS

Urinary NGAL and Creatinine were measured daily for up to 3 days. Doppler ultrasonography was performed within 24 h of admission and for the following 3 days.

RESULTS

Of the 21 patients, 44% had AKI during their ICU stay. The AKI group presented with higher values of serum Creatinine, renal length, MDRD as well as SAPS II already at admission. Urinary NGAL was significantly higher among patients with AKI and patients AKI-no at T0 (p < 0.0001) and increased steadily on T1 and T2. Urinary NGAL seemed to be a notable diagnostic marker for AKI from the first measurement (T0) with an area under the ROC of 0.93 (95% CI = 0.78-0.99) with a sensitivity of 99%. RRI levels were slightly higher in the AKI group at each time and increased gradually from T0 to T2 but reached statistical significance only at T2 (p = 0.02). Renal length and SAPS II at T0 showed high AuRoc and sensitivity.

CONCLUSIONS

Urinary NGAL is a valuable marker for AKI in intensive care settings. It seemed that a pre-existing chronic renal disease, the SAPS II and the NGAL at admission represented the principal predictors of AKI.

The Protective Pathways Activated in Kidneys of αMUPA Transgenic Mice Following Ischemia\Reperfusion-Induced Acute Kidney Injury

Despite the high prevalence of acute kidney injury (AKI), the therapeutic approaches for AKI are disappointing. This deficiency stems from the poor understanding of the pathogenesis of AKI. Recent studies demonstrate that αMUPA, alpha murine urokinase-type plasminogen activator (uPA) transgenic mice, display a cardioprotective pathway following myocardial ischemia. We hypothesize that these mice also possess protective renal pathways. Male and female αMUPA mice and their wild type were subjected to 30 min of bilateral ischemic AKI. Blood samples and kidneys were harvested 48 h following AKI for biomarkers of kidney function, renal injury, inflammatory response, and intracellular pathways sensing or responding to AKI. αMUPA mice, especially females, exhibited attenuated renal damage in response to AKI, as was evident from lower SCr and BUN, normal renal histology, and attenuated expression of NGAL and KIM-1. Notably, αMUPA females did not show a significant change in renal inflammatory and fibrotic markers following AKI as compared with wild-type (WT) mice and αMUPA males. Moreover, αMUPA female mice exhibited the lowest levels of renal apoptotic and autophagy markers during normal conditions and following AKI. αMUPA mice, especially the females, showed remarkable expression of PGC1α and eNOS following AKI. Furthermore, MUPA mice showed a significant elevation in renal leptin expression before and following AKI. Pretreatment of αMUPA with leptin-neutralizing antibodies prior to AKI abolished their resistance to AKI. Collectively, the kidneys of αMUPA mice, especially those of females, are less susceptible to ischemic I/R injury compared to WT mice, and this is due to nephroprotective actions mediated by the upregulation of leptin, eNOS, ACE2, and PGC1α along with impaired inflammatory, fibrotic, and autophagy processes.

Urinary proteome analysis of acute kidney injury in post-cardiac surgery patients using enrichment materials with high-resolution mass spectrometry

Background: Cardiac surgery-associated acute kidney injury (CSA-AKI) may increase the mortality and incidence rates of chronic kidney disease in critically ill patients. This study aimed to investigate the underlying correlations between urinary proteomic changes and CSA-AKI.

Methods: Nontargeted proteomics was performed using nano liquid chromatography coupled with Orbitrap Exploris mass spectrometry (MS) on urinary samples preoperatively and postoperatively collected from patients with CSA-AKI. Gemini C18 silica microspheres were used to separate and enrich trypsin-hydrolysed peptides under basic mobile phase conditions. Differential analysis was conducted to screen out urinary differential expressed proteins (DEPs) among patients with CSA-AKI for bioinformatics. Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis was adopted to identify the altered signal pathways associated with CSA-AKI.

Results: Approximately 2000 urinary proteins were identified and quantified through data-independent acquisition MS, and 324 DEPs associated with AKI were screened by univariate statistics. According to KEGG enrichment analysis, the signal pathway of protein processing in the endoplasmic reticulum was enriched as the most up-regulated DEPs, and cell adhesion molecules were enriched as the most down-regulated DEPs. In protein–protein interaction analysis, the three hub targets in the up-regulated DEPs were α-1-antitrypsin, β-2-microglobulin and angiotensinogen, and the three key down-regulated DEPs were growth arrest-specific protein 6, matrix metalloproteinase-9 and urokinase-type plasminogen activator.

Conclusion: Urinary protein disorder was observed in CSA-AKI due to ischaemia and reperfusion. The application of Gemini C18 silica microspheres can improve the protein identification rate to obtain highly valuable resources for the urinary DEPs of AKI. This work provides valuable knowledge about urinary proteome biomarkers and essential resources for further research on AKI.

Pulmonary haemorrhage as the earliest sign of severe leptospirosis in hamster model challenged with Leptospira interrogans strain HP358

Background

Severe leptospirosis is challenging as it could evolve rapidly and potentially fatal if appropriate management is not performed. An understanding of the progression and pathophysiology of Leptospira infection is important to determine the early changes that could be potentially used to predict the severe occurrence of leptospirosis. This study aimed to understand the kinetics pathogenesis of Leptospira interrogans strain HP358 in the hamster model and identify the early parameters that could be used as biomarkers to predict severe leptospirosis.

Methodology/Principal findings

Male Syrian hamsters were infected with Leptospira interrogans strain HP358 and euthanized after 24 hours, 3, 4, 5, 6 and 7 days post-infection. Blood, lungs, liver and kidneys were collected for leptospiral detection, haematology, serum biochemistry and differential expression of pro- and anti-inflammatory markers. Macroscopic and microscopic organ damages were investigated. Leptospira interrogans strain HP358 was highly pathogenic and killed hamsters within 6–7 days post-infection. Pulmonary haemorrhage and blood vessel congestion in organs were noticed as the earliest pathological changes. The damages in organs and changes in biochemistry value were preceded by changes in haematology and immune gene expression.

Conclusion/Significance

This study deciphered haemorrhage as the earliest manifestation of severe leptospirosis and high levels of IL-1β, CXCL10/IP-10, CCL3/MIP-α, neutrophils and low levels of lymphocytes and platelets serve as a cumulative panel of biomarkers in severe leptospirosis.

As the severe form of leptospirosis could progress rapidly and be potentially fatal if not treated earlier, deciphering the pathophysiology kinetics of infection is crucial to determine the parameters of disease severity. To understand this, we challenged hamsters with the highly virulent Leptospira interrogans strain HP358. Pulmonary haemorrhage was observed as the earliest pathological change followed by liver and kidneys damages. The increased expression of IL-1β, CXCL10/IP-10, CCL3/MIP-α, high neutrophils and low lymphocytes and platelets production observed in the present study indicate that these parameters could serve as a cumulative panel of biomarkers in severe leptospirosis.

Use of Ultra High Performance Liquid Chromatography with High Resolution Mass Spectrometry to Analyze Urinary Metabolome Alterations Following Acute Kidney Injury in Post-Cardiac Surgery Patients

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Cardiac surgery-associated AKI results in dramatic changes in urinary metabolome.

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Urinary metabolite disorder observed in patients with cardiac surgery-associated AKI.

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When metaboloite disorder was due to ischaemia and medical treatment, kidneys could return to normal.

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This work provides data about urinary metabolic profiles and resources for further research on AKI.

Background

Cardiac surgery-associated acute kidney injury (AKI) can increase the mortality and morbidity, and the incidence of chronic kidney disease, in critically ill survivors. The purpose of this research was to investigate possible links between urinary metabolic changes and cardiac surgery-associated AKI.

Methods

Using ultra-high-performance liquid chromatography coupled with Q-Exactive Orbitrap mass spectrometry, non-targeted metabolomics was performed on urinary samples collected from groups of patients with cardiac surgery-associated AKI at different time points, including Before_AKI (uninjured kidney), AKI_Day1 (injured kidney) and AKI_Day14 (recovered kidney) groups. The data among the three groups were analyzed by combining multivariate and univariate statistical methods, and urine metabolites related to AKI in patients after cardiac surgery were screened. Altered metabolic pathways associated with cardiac surgery-induced AKI were identified by examining the Kyoto Encyclopedia of Genes and Genomes database.

Results

The secreted urinary metabolome of the injured kidney can be well separated from the urine metabolomes of uninjured or recovered patients using multivariate and univariate statistical analyses. However, urine samples from the AKI_Day14 and Before_AKI groups cannot be distinguished using either of the two statistical analyses. Nearly 4000 urinary metabolites were identified through bioinformatics methods at Annotation Levels 1–4. Several of these differential metabolites may also perform essential biological functions. Differential analysis of the urinary metabolome among groups was also performed to provide potential prognostic indicators and changes in signalling pathways. Compared with the uninjured kidney group, the patients with cardiac surgery-associated AKI displayed dramatic changes in renal metabolism, including sulphur metabolism and amino acid metabolism.

Conclusions

Urinary metabolite disorder was observed in patients with cardiac surgery-associated AKI due to ischaemia and medical treatment, and the recovered patients’ kidneys were able to return to normal. This work provides data on urine metabolite markers and essential resources for further research on AKI.

Urinary Extracellular Vesicles: Uncovering the Basis of the Pathological Processes in Kidney-Related Diseases

Intercellular communication governs multicellular interactions in complex organisms. A variety of mechanisms exist through which cells can communicate, e.g., cell-cell contact, the release of paracrine/autocrine soluble molecules, or the transfer of extracellular vesicles (EVs). EVs are membrane-surrounded structures released by almost all cell types, acting both nearby and distant from their tissue/organ of origin. In the kidney, EVs are potent intercellular messengers released by all urinary system cells and are involved in cell crosstalk, contributing to physiology and pathogenesis. Moreover, urine is a reservoir of EVs coming from the circulation after crossing the glomerular filtration barrier—or originating in the kidney. Thus, urine represents an alternative source for biomarkers in kidney-related diseases, potentially replacing standard diagnostic techniques, including kidney biopsy. This review will present an overview of EV biogenesis and classification and the leading procedures for isolating EVs from body fluids. Furthermore, their role in intra-nephron communication and their use as a diagnostic tool for precision medicine in kidney-related disorders will be discussed.

Clinical assessment and pathophysiology of Bothrops venom-related acute kidney injury: a scoping review

Bothrops are one of the most common medically important snakes found in Latin America. Its venom is predominantly hemotoxic and proteolytic, which means that local lesion (edema and redness) and hemorrhagic symptoms are recurrent in envenoming by this snake. Although hemorrhage is usually the major cause of death, snakebite-related acute kidney injury is another potentially fatal clinical complication that may lead to chronic kidney disease. The present review highlights the main studies on Bothrops venom-related acute kidney injury, including observational, cross-sectional, case-control and cohort human studies available up to December 2019. The following descriptors were used according to Medical Subject Headings (MeSH): on Medline/Pubmed and Google Scholar "acute kidney injury" or "kidney disease" and "Bothrops"; on Lilacs and SciELO "kidney disease" or "acute kidney injury" and "Bothrops". Newcastle-Ottawa quality assessment scale was used to appraise the quality of the cross-sectional and cohort studies included. The selection of more severe patients who looked for health care units and tertiary centers is a risk of bias. Due to the methodological heterogeneity of the studies, a critical analysis of the results was performed based on the hypothesis that the design of the included studies influences the incidence of acute kidney injury. Fifteen human studies (total participants 4624) were included according to stablished criteria. The coagulation abnormalities (hemorrhagic symptoms, abnormal fibrinogen and activated partial thromboplastin time) were associated with acute kidney injury in the most recent studies reported. The findings observed in this review provide up-to-date evidence about the acute kidney injury pathogenesis following Bothrops syndrome. Studies pointed out that coagulation abnormalities comprise the major pathway for acute kidney injury development. This review may improve patient management by primary healthcare providers, allowing earlier diagnosis and treatment of Bothrops venom-related acute kidney injury.

LC-MS-based metabolomics analysis to identify meprin-β-associated changes in kidney tissue from mice with STZ-induced type 1 diabetes and diabetic kidney injury

Meprin metalloproteases have been implicated in the pathophysiology of diabetic kidney disease (DKD). Single-nucleotide polymorphisms in the meprin-β gene have been associated with DKD in Pima Indians, a Native American ethnic group with an extremely high prevalence of DKD. In African American men with diabetes, urinary meprin excretion positively correlated with the severity of kidney injury. In mice, meprin activity decreased at the onset of diabetic kidney injury. Several studies have identified meprin targets in the kidney. However, it is not known how proteolytic processing of the targets by meprins impacts the metabolite milieu in kidneys. In the present study, global metabolomics analysis identified differentiating metabolites in kidney tissues from wild-type and meprin-β knockout mice with streptozotocin (STZ)-induced type 1 diabetes. Kidney tissues were harvested at 8 wk post-STZ and analyzed by hydrophilic interaction liquid chromatography ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Principal component analysis identified >200 peaks associated with diabetes. Meprin expression-associated metabolites with strong variable importance of projection scores were indoxyl sulfate, N-γ-l-glutamyl-l-aspartic acid, N-methyl-4-pyridone-3-carboxamide, inosine, and cis-5-decenedioic acid. N-methyl-4-pyridone-3-carboxamide has been previously implicated in kidney injury, and its isomers, 4-PY and 2-PY, are markers of peroxisome proliferation and inflammation that correlate with creatinine clearance and glucose tolerance. Meprin deficiency-associated differentiating metabolites with high variable importance of projection scores were cortisol, hydroxymethoxyphenylcarboxylic acid-O-sulfate, and isovaleryalanine. The data suggest that meprin-β activity enhances diabetic kidney injury in part by altering the metabolite balance in kidneys, favoring high levels of uremic toxins such as indoxyl sulfate and N-methyl-pyridone-carboxamide.

Acute kidney injury overview: From basic findings to new prevention and therapy strategies

Acute kidney injury (AKI) is defined as a decrease in kidney function within hours, which encompasses both injury and impairment of renal function. AKI is not considered a pathological condition of single organ failure, but a syndrome in which the kidney plays an active role in the progression of multi-organ dysfunction. The incidence rate of AKI is increasing and becoming a common (8-16% of hospital admissions) and serious disease (four-fold increased hospital mortality) affecting public health costs worldwide. AKI also affects the young and previously healthy individuals affected by infectious diseases in Latin America. Because of the multifactorial pathophysiological mechanisms, there is no effective pharmacological therapy that prevents the evolution or reverses the injury once established; therefore, renal replacement therapy is the only current alternative available for renal patients. The awareness of an accurate and prompt recognition of AKI underlying the various clinical phenotypes is an urgent need for more effective therapeutic interventions to diminish mortality and socio-economic impacts of AKI. The use of biomarkers as an indicator of the initial stage of the disease is critical and the cornerstone to fulfill the gaps in the field. This review discusses emerging strategies from basic science toward the anticipation of features, treatment of AKI, and new treatments using pharmacological and stem cell therapies. We will also highlight bioartificial kidney studies, addressing the limitations of the development of this innovative technology.

A clinical, proteomics, and artificial intelligence-driven model to predict acute kidney injury in patients undergoing coronary angiography

Background

Standard measures of kidney function are only modestly useful for accurate prediction of risk for acute kidney injury (AKI).

Hypothesis

Clinical and biomarker data can predict AKI more accurately.

Methods

Using Luminex xMAP technology, we measured 109 biomarkers in blood from 889 patients prior to undergoing coronary angiography. Procedural AKI was defined as an absolute increase in serum creatinine of ≥0.3 mg/dL, a percentage increase in serum creatinine of ≥50%, or a reduction in urine output (documented oliguria of <0.5 mL/kg per hour for >6 hours) within 7 days after contrast exposure. Clinical and biomarker predictors of AKI were identified using machine learning and a final prognostic model was developed with least absolute shrinkage and selection operator (LASSO).

Results

Forty‐three (4.8%) patients developed procedural AKI. Six predictors were present in the final model: four (history of diabetes, blood urea nitrogen to creatinine ratio, C‐reactive protein, and osteopontin) had a positive association with AKI risk, while two (CD5 antigen‐like and Factor VII) had a negative association with AKI risk. The final model had a cross‐validated area under the receiver operating characteristic curve (AUC) of 0.79 for predicting procedural AKI, and an in‐sample AUC of 0.82 (P < 0.001). The optimal score cutoff had 77% sensitivity, 75% specificity, and a negative predictive value of 98% for procedural AKI. An elevated score was predictive of procedural AKI in all subjects (odds ratio = 9.87; P < 0.001).

Conclusions

We describe a clinical and proteomics‐supported biomarker model with high accuracy for predicting procedural AKI in patients undergoing coronary angiography.

NMR spectroscopy and electron microscopy identification of metabolic and ultrastructural changes to the kidney following ischemia-reperfusion injury

Cellular, molecular, and ultrastructural nephron changes associated with ischemia-reperfusion injury-induced acute kidney injury (IRI-AKI) are not completely understood. Here, a multidisciplinary study was used to identify nephron changes in a mouse model of IRI-AKI. Histological analyses indicated distended Bowman's glomerular spaces and proximal and distal tubules. Increased filtrate volume in nephrons was caused by reduced water reabsorption by severely damaged proximal tubule brush borders and blocked flow of filtrate into collecting tubules by mucoprotein casts in distal tubules. Immunohistochemistry revealed protein AKI biomarkers in proximal tubules and glomeruli but not in distal tubules. Nuclear magnetic resonance spectroscopy revealed several metabolites that increased such as valine, alanine, and lactate. Other metabolites such as trigonelline, succinate, 2-oxoisocaproate, and 1- methyl-nicotinamide decreased or were absent in urine following IRI due to altered kidney function or metabolism. Urinary glucose increased due to reduced reabsorption by damaged proximal tubule brush borders. Scanning electron microscopy revealed flattening of podocytes and pedicals surrounding glomerular capillaries, and transmission electron microscopy (TEM) revealed effacement of podocyte pedicals, both consistent with increased hydrostatic pressure in nephrons following IRI-AKI. TEM revealed shortened proximal tubule microvilli in IRI kidneys with diminished lamina propia. TEM showed dramatic loss of mitochondria in distal tubule epithelia of IRI kidneys and emergence of multivesicular bodies of endosomes indicating ongoing cellular death. Collectively, the data define ultrastructural changes to nephrons and altered kidney metabolism associated with IRI-AKI.

Biomarkers for childhood-onset systemic lupus erythematosus

Childhood-onset systemic lupus erythematosus (cSLE) is a systemic autoimmune disease characterized by the presence of autoantibodies. cSLE often affects multiple organs in the body and is known to have a poorer prognosis than adult-onset disease (Azevedo et al. 2014). Current laboratory tests are clearly insufficient for identifying and monitoring the disease. Recent studies have yielded novel biomarkers for cSLE which can be used for monitoring disease activity and response to treatment. The most encouraging biomarkers will be discussed herein and include cell-bound complement activation products, some genomic profiles, and urinary proteins such as neutrophil gelatinase-associated lipocalin, monocyte chemoattractant protein-1, and others. Previous studies suggested that a combination of the novel biomarkers might help to enhance sensitivity and specificity for early diagnosis, disease monitoring, and prediction of cSLE flares.

The use of biophysical proteomic techniques in advancing our understanding of diseases

The use of proteomic approaches in investigating diseases is continuing to expand and has started to provide answers to substantial gaps in our understanding of disease pathogenesis as well as in the development of effective strategies for the early diagnosis and treatment of diseases. Biophysical techniques form a crucial part of the advanced proteomic techniques currently used and include mass spectrometry and protein separation techniques, such as two-dimensional gel electrophoresis and liquid chromatography. The application of biophysical proteomic techniques in the study of disease includes delineation of altered protein expression, not only at the whole-cell or tissue levels, but also in subcellular structures, protein complexes, and biological fluids. These techniques are also being used for the discovery of novel disease biomarkers, exploration of the pathogenesis of diseases, development of new diagnostic methodologies, and identification of new targets for therapeutics. Proteomic techniques also have the potential for accelerating drug development through more effective strategies for evaluating a specific drug's therapeutic effects and toxicity. This article discusses the application of biophysical proteomic techniques in delineating cardiovascular disease and other diseases, as well as the limitations and future research directions required for these techniques to gain greater acceptance and have a larger impact.

Marking renal injury: can we move beyond serum creatinine?

Acute kidney injury (AKI) is a prevalent and devastating condition associated with significant morbidity and mortality. Despite marked improvements in clinical care, the outcomes for subjects with AKI have shown limited improvement in the past 50 years. A major factor inhibiting clinical progress in this field has been the inability to accurately predict and diagnose early kidney dysfunction. The current gold standard clinical and biochemical criteria for diagnosis of AKI, Risk Injury Failure Loss End-stage renal disease, and its modification, Acute Kidney Injury Network criteria, rely on urine output and serum creatinine, which are insensitive, nonspecific, and late markers of disease. The recent development of a variety of analytic mass spectrometry-based platforms have enabled separation, characterization, detection, and quantification of proteins (proteomics) and metabolites (metabolomics). These high-throughput platforms have raised hopes of identifying novel protein and metabolite markers, and recent efforts have led to several promising novel markers of AKI. However, substantial challenges remain, including the need to systematically evaluate incremental performance of these markers over and beyond current clinical and biochemical criteria for AKI. We discuss the basic issues surrounding AKI biomarker development, highlight the most promising markers currently under development, and discuss the barriers toward widespread clinical implementation of these markers.