Proteomic identification of early urinary-biomarkers of acute kidney injury in preterm infants

Host-derived protein profiles of human neonatal meconium across gestational ages

Meconium, a non-invasive biomaterial reflecting prenatal substance accumulation, could provide valuable insights into neonatal health. However, the comprehensive protein profile of meconium across gestational ages remains unclear. Here, we conducted an extensive proteomic analysis of first meconium from 259 newborns across varied gestational ages to delineate protein composition and elucidate its relevance to neonatal diseases. The first meconium samples were collected, with the majority obtained before feeding, and the mean time for the first meconium passage from the anus was 11.9 ± 9.47 h. Our analysis revealed 5370 host-derived meconium proteins, which varied depending on sex and gestational age. Specifically, meconium from preterm infants exhibited elevated concentrations of proteins associated with the extracellular matrix. Additionally, the protein profiles of meconium also exhibited unique variations depending on both specific diseases, including gastrointestinal diseases, congenital heart diseases, and maternal conditions. Furthermore, we developed a machine learning model to predict gestational ages using meconium proteins. Our model suggests that newborns with gastrointestinal diseases and congenital heart diseases may have immature gastrointestinal systems. These findings highlight the intricate relationship between clinical parameters and meconium protein composition, offering potential for a novel approach to assess neonatal gastrointestinal health.

The Relevance, Predictability, and Utility of Annexin A5 for Human Physiopathology

As an important functional protein molecule in the human body, human annexin A5 (hAnxA5) is widely found in human cells and body fluids. hAnxA5, the smallest type of annexin, performs a variety of biological functions by reversibly and specifically binding phosphatidylserine (PS) in a calcium-dependent manner and plays an important role in many human physiological and pathological processes. The free state hAnxA5 exists in the form of monomers and usually forms a polymer in a specific self-assembly manner when exerting biological activity. This review systematically discusses the current knowledge and understanding of hAnxA5 from three perspectives: physiopathological relevance, diagnostic value, and therapeutic utility. hAnxA5 affects the occurrence and development of many physiopathological processes. Moreover, hAnxA5 can be used independently or in combination as a biomarker of physiopathological phenomena for the diagnosis of certain diseases. Importantly, based on the properties of hAnxA5, many novel drug candidates have been designed and prepared for application in actual medical practice. However, there are also some gaps and shortcomings in hAnxA5 research. This in-depth study will not only expand the understanding of structural and functional relationships but also promote the application of hAnxA5 in the field of biomedicine.

Gestational Age-Related Urinary Peptidome Changes in Preterm and Term Born Infants

INTRODUCTION

Preterm infants are at risk for a variety of somatic and neurological disorders. In recent years, biofluid proteomics has emerged as a potential diagnostic tool for biomarker analysis. The aim of this study was to determine gestational age (GA)-related patterns of the urinary peptidome in preterm infants for researching potential novel prognostic biomarkers.

METHODS

We performed urinary peptidomics in longitudinal samples of 24 preterm (mean GA weeks 28 + 1 [24+1-31 + 6]) and 27 term born controls (mean GA weeks 39 + 2 [37+0-41 + 1]) using capillary electrophoresis combined with mass spectrometry (CE-MS). Peptides were sequenced using CE-MS/MS or LC-MS/MS analysis and were deposited, matched, and annotated in a Microsoft SQL database for statistical analysis. We compared their abundance in urine of preterm and term born infants and performed a validation analysis as well as correlations to GA and clinical risk scores.

RESULTS

Our results confirmed significant differences in the abundance of peptides and the hypothesis of age-dependent urinary peptidome changes in preterm and term infants. In preterm infants, SLC38A10 (solute carrier family 38 member 10) is one of the most abundant peptides. Combined urinary peptides correlated with clinical risk scores (p < 0.05).

CONCLUSION

This is the first study reporting GA-related urinary peptidome changes of preterm infants detected by CE-MS and a modulation of the peptidome with GA. Further research is required to locate peptidome clusters correlated with specific clinical complications and long-term outcome. This may identify preterm infants at higher risk for adverse outcome who would benefit from early intervention.

Recent Advances of Proteomics in Management of Acute Kidney Injury

Acute Kidney Injury (AKI) is currently recognized as a life-threatening disease, leading to an exponential increase in morbidity and mortality worldwide. At present, AKI is characterized by a significant increase in serum creatinine (SCr) levels, typically followed by a sudden drop in glomerulus filtration rate (GFR). Changes in urine output are usually associated with the renal inability to excrete urea and other nitrogenous waste products, causing extracellular volume and electrolyte imbalances. Several molecular mechanisms were proposed to be affiliated with AKI development and progression, ultimately involving renal epithelium tubular cell-cycle arrest, inflammation, mitochondrial dysfunction, the inability to recover and regenerate proximal tubules, and impaired endothelial function. Diagnosis and prognosis using state-of-the-art clinical markers are often late and provide poor outcomes at disease onset. Inappropriate clinical assessment is a strong disease contributor, actively driving progression towards end stage renal disease (ESRD). Proteins, as the main functional and structural unit of the cell, provide the opportunity to monitor the disease on a molecular level. Changes in the proteomic profiles are pivotal for the expression of molecular pathways and disease pathogenesis. Introduction of highly-sensitive and innovative technology enabled the discovery of novel biomarkers for improved risk stratification, better and more cost-effective medical care for the ill patients and advanced personalized medicine. In line with those strategies, this review provides and discusses the latest findings of proteomic-based biomarkers and their prospective clinical application for AKI management.

Urine acute kidney injury biomarkers in extremely low gestational age neonates: a nested case control study of 21 candidate urine biomarkers

BACKGROUND

Acute kidney injury (AKI) is common and is associated with poor clinical outcomes in premature neonates. Urine biomarkers hold the promise to improve our understanding and care of patients with kidney disease. Because kidney maturation and gender can impact urine biomarker values in extremely low gestational age neonates (ELGANs), careful control of gestational age (GA) and time is critical to any urine biomarker studies in neonates.

METHODS

To improve our understanding of the potential use of urine biomarkers to detect AKI during the first postnatal weeks, we performed a nested case-control study to evaluate 21 candidate urine AKI biomarkers. Cases include 20 ELGANs with severe AKI. Each case was matched with 2 controls for the same GA week (rounded down to the nearest week), gender, and birth weight (BW) (± 50 g).

RESULTS

Urine cystatin C, creatinine, ghrelin, fibroblast growth factor-23 (FGF23), tissue metalloproteinase 2 (TIMP2) and vascular endothelial growth factor A (VEGFa) concentrations were higher in ELGANs with early severe AKI compared to matched control subjects without AKI. Urine epidermal growth factor (EGF) and uromodulin (UMOD) concentrations are lower in cases than controls. Interleukin (IL)-15 was lower on day 1, but higher on day 8 in cases than controls; while VEGFa was lower on day 1, but higher on day 5 in cases than controls.

CONCLUSION

Urine biomarkers hold the promise to improve our ability to reliably detect kidney injury. Interventional studies are needed to determine the biomarkers' ability to predict outcomes, enhance AKI phenotypes, and improve timely interventions which can prevent the sequalae of AKI in ELGANs. A higher resolution version of the Graphical abstract is available as Supplementary information.

Serum and urinary biomarkers to predict acute kidney injury in premature infants: a systematic review and meta-analysis of diagnostic accuracy

BACKGROUND

Premature infants are at high risk for acute kidney injury (AKI) and current diagnostic criteria are flawed. The objective of this study was to determine the diagnostic accuracy of urine and serum biomarkers not currently used in routine clinical practice to predict AKI in premature infants.

METHOD

A systematic review was performed that followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses of Diagnostic Test Accuracy Studies (PRISMA-DTA). Data were extracted on the diagnostic accuracy of AKI biomarkers using serum creatinine or urine output as the reference standard. Quality and validity were assessed using modified Standards for Reporting Diagnostic Accuracy (STARD) criteria.

RESULTS

We identified 1024 articles, with 15 studies (791 infants) eligible for inclusion. Twenty-seven biomarkers were identified including serum cystatin C and urinary neutrophil gelatinase-associated lipocalin (uNGAL), osteopontin, kidney injury molecule-1, epidermal growth factor, and protein S100-P. However, many were only reported by one study each. A meta-analysis could only be conducted on uNGAL (288 infants from 6 studies) using a hierarchical, random-effects logistic-regression model. uNGAL had a summary sensitivity of 77% (95% CI 58-89%), specificity of 76% (95% CI 57-88%) and AUC-SROC of 0.83 (95% CI 0.80-0.86) for the diagnosis of AKI. By utilising uNGAL, the post-test probability of AKI increased to 52% (95% CI 37-66%) with a positive test and decreased to 9% (95% CI 5-16%) with a negative test if the pre-test probability was 25%.

CONCLUSION

uNGAL shows promise as a diagnostically accurate biomarker for AKI in premature infants.

Impact of nephrotoxic drugs on urinary biomarkers of renal function in very preterm infants

BACKGROUND

Following preterm birth, the immature kidney is exposed to several harmful conditions, with an increased risk of renal impairment. We aimed to assess urinary biomarkers of renal function in very preterm infants during early nephrotoxic treatments.

METHODS

Infants ≤32 weeks' gestation and ≤1500 g were enrolled in this observational prospective study. Urine samples were collected on day 1(T1), 2-4(T2), 5-7(T3), 8-10(T4), 11-13(T5). The following urinary biomarkers were determined: osteopontin (uOPN), epidermal growth factor (uEGF), neutrophil gelatinase-associated lipocalin (uNGAL), cystatin C (uCysC). The infants were grouped according to their exposure to amikacin or ibuprofen during the study period and a between-group comparison of urinary biomarkers at each time point was performed.

RESULTS

Thirty-six infants were included. Urinary CysC, uOPN, and uNGAL rose significantly during ibuprofen or amikacin treatment, while no difference was observed for uEGF. After adjustment for possible influencing factors, amikacin administration was associated with higher uCysC at T1 (p = 0.007) and T2 (p = 0.016), whereas ibuprofen increased uOPN (p = 0.001) and uNGAL concentration (p = 0.009) at T3.

CONCLUSION

Nephrotoxic therapies induce molecule-specific change patterns of renal function biomarkers in treated preterm infants. Serial assessments of these biomarkers may aid to identify neonates at risk of renal impairment and to develop tailored therapeutic approaches.

IMPACT

Despite the wide use of nephrotoxic therapies in neonatal settings, little is known on their effect on renal function biomarkers in preterm infants. This study describes molecule-specific change patterns of urinary biomarkers during ibuprofen and amikacin administration, suggesting underlying pathophysiological effects on renal function. Given their low analytical costs and non-invasive collection, the urinary biomarkers investigated in this study represent a promising strategy for serial monitoring of renal function in at-risk neonates and may aid the early detection of renal function impairment at different kidney levels during nephrotoxic treatments.

Isolation and Characterization of Urinary Extracellular Vesicles for MicroRNA Biomarker Signature Development with Reference to MISEV Compliance

Urine bears high potential for serving as biomarker repository for renal and urinary tract associated disorders. Besides various metabolites and salts, urine carries extracellular vesicles (EVs)-a heterogeneous group of cell-derived mediators comprising proteins, lipids, and nucleic acids such as microRNAs (miRNAs). Particularly, EV-derived miRNA biomarkers have already been identified for numerous disorders such as sepsis, various blood and solid cancer entities, respiratory and renal diseases. However, study results are often incomparable due to poorly reported EV separation and miRNA isolation protocols and emphasize the need for standardization and reproducibility. To ensure valid EV-derived miRNA biomarker findings from urine, a step-by-step protocol compliant with the "Minimal Information for Studies of Extracellular Vesicles" (MISEV) is outlined in the following paragraphs. Actually, an immunoaffinity-based EV separation method followed by EV characterization, quantification, and normalization, as well as consecutive miRNA isolation and miRNA profiling by small RNA sequencing, are described.

Management of Acute Kidney Injury in Extremely Low Birth Weight Infants

Acute kidney injury (AKI) is a common problem in the neonatal intensive care unit (NICU). Neonates born at <1,000 g (extremely low birth weight, ELBW) are at an increased risk of secondary associated comorbidities such as intrauterine growth restriction, prematurity, volume restriction, ischaemic injury, among others. Studies estimate up to 50% ELBW infants experience at least one episode of AKI during their NICU stay. Although no curative treatment for AKI currently exists, recognition is vital to reduce potential ongoing injury and mitigate long-term consequences of AKI. However, the definition of AKI is imperfect in this population and presents clinical challenges to correct identification, thus contributing to under recognition and reporting. Additionally, the absence of guidelines for the management of AKI in ELBW infants has led to variations in practice. This review summarizes AKI in the ELBW infant and includes suggestions such as close observation of daily fluid balance, review of medications to reduce nephrotoxic exposure, management of electrolytes, maximizing nutrition, and the use of diuretics and/or dialysis when appropriate.

HiPSC-Derived Hepatocyte-like Cells Can Be Used as a Model for Transcriptomics-Based Study of Chemical Toxicity

Traditional toxicity risk assessment approaches have until recently focussed mainly on histochemical readouts for cell death. Modern toxicology methods attempt to deduce a mechanistic understanding of pathways involved in the development of toxicity, by using transcriptomics and other big data-driven methods such as high-content screening. Here, we used a recently described optimised method to differentiate human induced pluripotent stem cells (hiPSCs) to hepatocyte-like cells (HLCs), to assess their potential to classify hepatotoxic and non-hepatotoxic chemicals and their use in mechanistic toxicity studies. The iPSC-HLCs could accurately classify chemicals causing acute hepatocellular injury, and the transcriptomics data on treated HLCs obtained by TempO-Seq technology linked the cytotoxicity to cellular stress pathways, including oxidative stress and unfolded protein response (UPR). Induction of these stress pathways in response to amiodarone, diclofenac, and ibuprofen, was demonstrated to be concentration and time dependent. The transcriptomics data on diclofenac-treated HLCs were found to be more sensitive in detecting differentially expressed genes in response to treatment, as compared to existing datasets of other diclofenac-treated in vitro hepatocyte models. Hence iPSC-HLCs generated by transcription factor overexpression and in metabolically optimised medium appear suitable for chemical toxicity detection as well as mechanistic toxicity studies.

Urinary proteomics investigations into contrast-induced acute kidney injury

Some patients have a decline in renal function after contrast medium injection, and this phenomenon is called contrast-induced acute kidney injury (CI-AKI); a small number of people even suffer severe renal failure. To date, the mechanism of CI-AKI remains unclear. We aimed to identify novel potential biomarkers in the urine of patients with CI-AKI through LC-MS/MS and bioinformatics analysis. We enrolled patients who underwent coronary angiography (contrast agent: iohexol). The CI-AKI group included 4 cases, and the non-CI-AKI group included 20 cases. We mixed the 4 CI-AKI samples and 20 non-CI-AKI samples. Then, a 0.6 ml urine sample was used for proteome analysis with LC-MS/MS approach. Metascape, ExPASy, and the Human Protein Atlas were utilized for bioinformatics analysis. We obtained 724 and 830 urine proteins from the CI-AKI and non-CI-AKI groups, respectively. The distribution of the pI values and molecular weights (MWs) of postoperative urine proteins showed no significant difference between the CI-AKI group and the non-CI-AKI group. A total of 99differentially expressed proteins (DEPs) were detected, among which 18 proteins were detected only in tubule cells, and 19 proteins were detected in both tubule cells and glomeruli. With GO analysis, the GEPs were mainly associated with immune response and inflammation. Although biomarkers cannot be asserted from this single pilot study, our results may help advance the understanding of the mechanisms of CI-AKI and identify potential novel biomarkers for further investigation.

Longitudinal Changes in Serum Creatinine Levels and Urinary Biomarkers in Late Preterm Infants during the First Postnatal Week: Association with Acute Kidney Injury and Treatment with Aminoglycoside

We aimed to determine the incidence of acute kidney injury (AKI) and longitudinal changes in SCr levels and urinary biomarkers associated with AKI and aminoglycoside (AG) medication during the first week of life of late preterm infants. Urine biomarkers and SCr were measured in thirty late preterm infants on days one, two, five, and seven postnatal. Urine biomarkers included neutrophil gelatinase-associated lipocalin (NGAL), monocyte chemotactic protein-1 (MCP-1), epidermal growth factor (EGF), Tamm-Horsfall glycoprotein (THP), and liver fatty-acid-binding protein (L-FABP). Gestational age was positively correlated with SCr levels at birth, but inversely correlated with SCr levels at day five and day seven. Eighteen (60%) infants had stage 1 AKI, and twenty (67%) infants were treated with AGs. Infants with AKI had lower gestational age and lower birth weight than those without AKI. Urinary biomarkers adjusted according to uCr levels in infants with AKI were not statistically different from those in infants without AKI. There were no significant differences in incidence of AKI, and SCr levels during and after cessation of AG treatment. The uMCP-1/Cr ratio at days five and seven was higher in infants treated with AG than in non-treated infants.

Urinary proteomics for kidney dysfunction: insights and trends

Introduction: Kidney dysfunction poses a high burden on patients and health care systems. Early detection and accurate prediction of kidney disease progression remains a major challenge. Compared to existing clinical parameters, urinary proteomics has the potential to reveal molecular alterations within the kidney that may alter its function before the onset of clinical symptoms. Thus, urinary proteomics has greater prognostic potential for assessment of kidney dysfunction progression.Areas covered: Advances in urinary proteomics for major causes of kidney dysfunction are discussed. The application of urinary extracellular vesicles for studying kidney dysfunction are discussed. Technological advances in urinary proteomics are discussed. The literature was identified using a database search for titles containing 'proteom*' and 'urin*' and published within the past 5 years. Retrieved literature was manually filtered to retain kidney dysfunctions-related studies.Expert opinion: Despite major advances, diagnosis by urinary proteomics has not been fully applied in any clinical settings. This could be attributed to the complex nature of kidney diseases, in addition to the constraints on study power and feasibility of incorporating mass spectrometry techniques in daily routine analysis. Nevertheless, we are confident that advances in urinary proteomics will soon provide superior insights into kidney disease beyond existing clinical parameters.

Perinatal Nutritional and Metabolic Pathways: Early Origins of Chronic Lung Diseases

Lung development is not completed at birth, but expands beyond infancy, rendering the lung highly susceptible to injury. Exposure to various influences during a critical window of organ growth can interfere with the finely-tuned process of development and induce pathological processes with aberrant alveolarization and long-term structural and functional sequelae. This concept of developmental origins of chronic disease has been coined as perinatal programming. Some adverse perinatal factors, including prematurity along with respiratory support, are well-recognized to induce bronchopulmonary dysplasia (BPD), a neonatal chronic lung disease that is characterized by arrest of alveolar and microvascular formation as well as lung matrix remodeling. While the pathogenesis of various experimental models focus on oxygen toxicity, mechanical ventilation and inflammation, the role of nutrition before and after birth remain poorly investigated. There is accumulating clinical and experimental evidence that intrauterine growth restriction (IUGR) as a consequence of limited nutritive supply due to placental insufficiency or maternal malnutrition is a major risk factor for BPD and impaired lung function later in life. In contrast, a surplus of nutrition with perinatal maternal obesity, accelerated postnatal weight gain and early childhood obesity is associated with wheezing and adverse clinical course of chronic lung diseases, such as asthma. While the link between perinatal nutrition and lung health has been described, the underlying mechanisms remain poorly understood. There are initial data showing that inflammatory and nutrient sensing processes are involved in programming of alveolarization, pulmonary angiogenesis, and composition of extracellular matrix. Here, we provide a comprehensive overview of the current knowledge regarding the impact of perinatal metabolism and nutrition on the lung and beyond the cardiopulmonary system as well as possible mechanisms determining the individual susceptibility to CLD early in life. We aim to emphasize the importance of unraveling the mechanisms of perinatal metabolic programming to develop novel preventive and therapeutic avenues.

A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer

Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers in the literature-curated database. Forty-three percentage of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.

Assessment of Inflammatory Markers in Children with Cow's Milk Allergy Treated with a Milk-Free Diet

Background: The aim of the study was to establish whether the use of a strict milk-free diet in children with cow’s milk allergy, resulting in the resolution of clinical symptoms of the disease, also extinguishes the inflammatory reaction induced by the allergy. Methods: We examined 64 children (aged 3–6 years) with a diagnosed cow’s milk allergy who had been treated with an elimination diet for at least six months and showed remission of the disease’s clinical symptoms as a result of the treatment. The control group consisted of 30 healthy children of the same age following an unrestricted age-appropriate diet. Concentrations of cytokines, calprotectin, and adipokines (leptin, resistin, chemerin, neutrophilic lipocalin associated with gelatinase—NGAL) were determined in the serum samples obtained from the studied children by immunoenzymatic assays. Results: Patients with CMA had significantly higher median values of serum IL-6, TNF-α, resistin, chemerin and NGAL in comparison to the healthy children (p < 0.05, p < 0.001, p < 0.05, p < 0.01, p < 0.001, respectively). Serum concentrations of IL-10, leptin, calprotectin and CRP as well as in WBC count were in the same range in both studied groups. We observed direct statistically significant correlations between levels of IL-10 and CRP (p = 0.005), IL-10 and WBC (p = 0.045), TNF-α and WBC (p = 0.038), calprotectin and WBC (p < 0.001), chemerin and CRP (p < 0.001) as well as between NGAL and WBC (p = 0.002) in children with CMA. Conclusion: The use of a strict milk-free diet by children with CMA, resulting in the resolution of clinical symptoms of the disease, does not seem to extinguish the inflammation induced by the allergy. The findings of this study—elevated IL-6, TNF-α, resistin, chemerin and NGAL levels in patients with CMA—suggest that these parameters seem to be involved in the generation of a low-grade proinflammatory environment observed in cow‘s milk allergy and could be used to monitor the effectiveness of treatment.

The tip of the iceberg for diagnostic dilemmas: Performance of current diagnostics and future complementary screening approaches

Genetic testing is currently the leading edge of clinical care when it comes to diagnostics. However, many questions remain unanswered even when employing next-generation sequencing techniques due to our inability to decode genetic variations and our limited repertoire of available diagnoses. Accordingly, diagnostic yields for current genomic screenings are <50% and fail to provide the whole picture, leaving the remaining patients without a definitive diagnosis. Human phenotypic/disease expression is explained by alterations not only at the genome, but also at the transcriptome, proteome and metabolome levels. These "higher" complexity levels represent at wealth of information, and diagnostic screenings tests at these levels have been shown to significantly improve diagnostic yields in specific populations compared to conventional diagnostic workup or gold standards in use (7-30% increase in diagnostic yields, depending on the population, approach and gold standard being compared against). However, these are not yet routinely available to clinicians. Due to their dynamic and modifiable nature, tapping into data from different omics will improve our understanding of the pathophysiological bases underlying (many yet to characterize) human disorders. We herein review how alterations at these levels (e.g. post-transcriptional and post-translational) may be pathogenic, how such tests may be implemented and in which situations they are of significant utility.