Strikingly conserved gene expression changes of polyamine regulating enzymes among various forms of acute and chronic kidney injury

Identification and Validation of Tryptophan Metabolism-Related Genes in Diabetic Kidney Disease and Construction of a Clinical Prediction Model

Background: Diabetic kidney disease (DKD) is a common microvascular complication of diabetes mellitus (DM). Amino acid (AA) homeostasis has an important impact on renal hemodynamics and glomerular hyperfiltration in patients with DKD, and the metabolite level of tryptophan (TRP), an AA, has been associated with various diseases. Methods: In this study, DKD tubule- and glomerulus-related microarray datasets were collected from the GEO database, and DKD-related modular genes were identified by weighted gene coexpression network analysis (WGCNA). TRP metabolism-related genes (TRGs) were downloaded from the MSigDB database, and the key genes were obtained by taking the intersection of DKD differentially expressed genes, TRGs, and modular genes. Validated with the Nephrseq v5 database and performed clinical prediction model construction. The association of pivotal genes with immune cell infiltration was verified using CIBERSORTx software. The protein expression of the key genes was verified by qPCR, Western blot, immunohistochemistry, and immunofluorescence. Results: Four hundred and seventy seven DEGs were identified in the GSE30529 dataset, 392 DEGs were identified in the GSE30528 dataset, and the intersection of the DEGs in the two datasets, the module with the most significant correlation with DKD obtained by WGCNA, and the TRGs were taken, respectively. Five key genes were finally obtained (AOC1, HAAO, STAT1, OGDHL, and TDO2). Compared with control-group mice, the expression of AOC1, HAAO, and OGDHL was significantly downregulated, and the expression of STAT1 and TDO2 was significantly elevated in DKD mice. The diagnostic model was constructed using the key genes AUC = 0.996. Conclusion: Our study suggests that the AOC1, HAAO, and STAT1 genes may be potential diagnostic biomarkers of tubular injury in DKD. OGDHL and TDO2 may be potential diagnostic biomarkers of glomerular injury in DKD. The model constructed using AOC1, HAAO, STAT1, OGDHL, and TDO2 had good disease differentiation.

Association of Serum Polyamines with Cardiovascular Events and All-Cause Mortality in Chronic Kidney Disease

BACKGROUND

Emerging evidence indicates that serum polyamines, including putrescine, spermidine, and spermine, may serve as potential biomarkers for chronic kidney disease (CKD) and its progression. However, the association between serum polyamine levels, cardiovascular (CV) events, and mortality in CKD patients remains poorly understood.

METHODS

A retrospective cohort study was conducted, involving 297 adult patients with CKD at stages 1-5 from March 2015 to September 2018, with follow-up until May 2023. Serum polyamine levels were quantified using high-performance liquid chromatography and subsequently categorized into quartiles. The Kaplan-Meier curve was employed to assess the survival probabilities of CV events and overall mortality in relation to serum polyamine levels. The relationship between serum polyamines and the risk of cardiovascular disease (CVD) and overall mortality was explored using univariate and multivariate Cox regression analyses. Furthermore, we conducted a competing-risk analysis to investigate the link between serum polyamines and CV events, with mortality as the competing event.

RESULTS

Over a median follow-up of 6.11 years, our findings revealed a negative correlation between putrescine levels and estimated glomerular filtration rate (eGFR), while spermidine and spermine levels were positively correlated with eGFR. The Kaplan-Meier curve demonstrated that serum polyamines were significantly associated with risk of CV events and all-cause mortality. Moreover, Cox regression analyses showed that, in a multivariate Cox model, patients in the highest quartile of putrescine displayed a significantly higher risk of CV events (hazard ratio [HR] 6.972, 95% confidence interval [CI] 2.520-19.294, p < 0.001) compared to those in the lowest quartile. Conversely, higher levels of spermidine were associated with a lower risk of CV events (HR = 0.077, 95% CI 0.022-0.274, p < 0.001), and higher levels of spermine also appeared to reduce the risk of CV events (HR = 0.180, 95% CI 0.061-0.530, p = 0.002). The relationship between serum polyamines and CVD remained robust in the competing risk models. Additionally, in the multivariate model, spermidine and spermine showed a significant protective effect on the risk of overall mortality; however, the protective effect was diminished upon the inclusion of eGFR as a covariate.

CONCLUSIONS

Our study demonstrates significant disruption in serum polyamine levels among CKD patients, which correlates with eGFR. Altered polyamine levels are linked to an increased risk of CV events and overall mortality. Thus, serum polyamines may be considered valuable prognostic indicators for CKD patients.

Polydopamine-Mediated, Centrifugal Force-Driven Gold Nanoparticle-Deposited Microneedle SERS Sensors for Food Safety Monitoring Theoretical Study of the SERS Substrate Fabrication

Microneedle (MN) sensors have great promise for food safety detection, but the rapid preparation of MNs for surface-enhanced Raman scattering (SERS) sensors with tunable and homogeneous nanoparticles remains a great challenge. To address this, a SERS sensor of gold nanoparticles@polydopamine@poly(methyl methacrylate) MN (AuNPs@PDA@PMMA-MN) was developed. The extended-Derjaguin-Landau-Verwey-Overbeek theory was applied to calculate the interaction energy between AuNPs and PDA. It was confirmed that an appropriate centrifugal force could be utilized to overcome the electrostatic repulsion between AuNPs and PDA. Together with the adhesion force of PDA, AuNPs can therefore be uniformly and densely deposited on the MN substrate. The AuNPs@PDA@PMMA-MN had an enhancement factor of up to 1.74 × 106 for R6G. Furthermore, a MN sensor for the selective detection of putrescine and cadaverine was successfully constructed by modifying 4-mercaptobenzaldehyde (4-MBA) on AuNPs@PDA@PMMA-MN substrates. This sensor could quantitatively detect putrescine and cadaverine in meat. It has been successfully applied to the in situ detection of putrescine and cadaverine in real meat samples. The AuNPs@PDA@PMMA-MN SERS sensor has the advantages of facile fabrication, high sensitivity, high specificity, and online, in situ detection capability. It is expected to have applications in food quality testing, environmental monitoring, and disease diagnosis.

Amino acid metabolism in kidney health and disease

Amino acids form peptides and proteins and are therefore considered the main building blocks of life. The kidney has an important but under-appreciated role in the synthesis, degradation, filtration, reabsorption and excretion of amino acids, acting to retain useful metabolites while excreting potentially harmful and waste products from amino acid metabolism. A complex network of kidney transporters and enzymes guides these processes and moderates the competing concentrations of various metabolites and amino acid products. Kidney amino acid metabolism contributes to gluconeogenesis, nitrogen clearance, acid-base metabolism and provision of fuel for tricarboxylic acid cycle and urea cycle intermediates, and is thus a central hub for homeostasis. Conversely, kidney disease affects the levels and metabolism of a variety of amino acids. Here, we review the metabolic role of the kidney in amino acid metabolism and describe how different diseases of the kidney lead to aberrations in amino acid metabolism. Improved understanding of the metabolic and communication routes that are affected by disease could provide new mechanistic insights into the pathogenesis of kidney diseases and potentially enable targeted dietary or pharmacological interventions.

Exploring Cuproptosis-Related Genes and Diagnostic Models in Renal Ischemia-Reperfusion Injury Using Bioinformatics, Machine Learning, and Experimental Validation

Background

Renal ischemia-reperfusion injury (RIRI) is a significant cause of acute kidney injury, complicating clinical interventions such as kidney transplants and partial nephrectomy. Recent research has indicated the role of cuproptosis, a copper-dependent cell death pathway, in various pathologies, but its specific involvement in RIRI remains insufficiently understood. This study aims to investigate the role of cuproptosis-related genes in RIRI and establish robust diagnostic models.

Methods

We analyzed transcriptomic data from 203 RIRI and 188 control samples using bioinformatics tools to identify cuproptosis-related differentially expressed genes (CRDEGs). The relationship between CRDEGs and immune cells was explored using immune infiltration analysis and correlation analysis. Gene Set Enrichment Analysis (GSEA) was conducted to identify pathways associated with CRDEGs. Machine learning models, including Least Absolute Shrinkage and Selection Operator(LASSO) logistic regression, Support Vector Machine Recursive Feature Elimination (SVM-RFE), Clustering analysis, and weighted gene co-expression network analysis (WGCNA), were used to construct diagnostic gene models. The models were validated using independent datasets. Experimental validation was conducted in vivo using a mouse bilateral RIRI model and in vitro using an HK-2 cell hypoxia-reoxygenation (HR) model with copper chelation intervention. HE, PAS, and TUNEL staining, along with plasma creatinine and blood urea nitrogen (BUN) measurements, were used to evaluate the protective effect of the copper chelator D-Penicillamine (D-PCA) on RIRI in mice. JC-1 and TUNEL staining were employed to assess apoptosis in HK-2 cells under hypoxia-reoxygenation conditions. Immunofluorescence and Western blot (WB) techniques were used to verify the expression levels of the SDHB and NDUFB6 genes.

Results

A total of 18 CRDEGs were identified, many of which were significantly correlated with immune cell infiltration. GSEA revealed that these genes were involved in pathways related to oxidative phosphorylation and immune response regulation. Four key cuproptosis marker genes (LIPA, LIPT1, SDHB, and NDUFB6) were incorporated into a Cuproptosis Marker Gene Model(CMGM), achieving an area under the curve (AUC) of 0.741-0.834 in validation datasets. In addition, a five-hub-gene SVM model (MOAP1, PPP2CA, SYL2, ZZZ3, and SFRS2) was developed, demonstrating promising diagnostic performance. Clustering analysis revealed two RIRI subtypes (C1 and C2) with distinct molecular profiles and pathway activities, particularly in oxidative phosphorylation and immune responses. Experimental results showed that copper chelation alleviated renal damage and cuproptosis in both in vivo and in vitro models.

Conclusion

Our study reveals that cuproptosis-related genes are significantly involved in RIRI, particularly influencing mitochondrial dysfunction and immune responses. The diagnostic models developed showed promising predictive performance across independent datasets. Copper chelation demonstrated potential therapeutic effects, suggesting that cuproptosis regulation may be a viable therapeutic strategy for RIRI. This work provides a foundation for further exploration of copper metabolism in renal injury contexts.

Inflammation primes the murine kidney for recovery by activating AZIN1 adenosine-to-inosine editing

The progression of kidney disease varies among individuals, but a general methodology to quantify disease timelines is lacking. Particularly challenging is the task of determining the potential for recovery from acute kidney injury following various insults. Here, we report that quantitation of post-transcriptional adenosine-to-inosine (A-to-I) RNA editing offers a distinct genome-wide signature, enabling the delineation of disease trajectories in the kidney. A well-defined murine model of endotoxemia permitted the identification of the origin and extent of A-to-I editing, along with temporally discrete signatures of double-stranded RNA stress and adenosine deaminase isoform switching. We found that A-to-I editing of antizyme inhibitor 1 (AZIN1), a positive regulator of polyamine biosynthesis, serves as a particularly useful temporal landmark during endotoxemia. Our data indicate that AZIN1 A-to-I editing, triggered by preceding inflammation, primes the kidney and activates endogenous recovery mechanisms. By comparing genetically modified human cell lines and mice locked in either A-to-I-edited or uneditable states, we uncovered that AZIN1 A-to-I editing not only enhances polyamine biosynthesis but also engages glycolysis and nicotinamide biosynthesis to drive the recovery phenotype. Our findings implicate that quantifying AZIN1 A-to-I editing could potentially identify individuals who have transitioned to an endogenous recovery phase. This phase would reflect their past inflammation and indicate their potential for future recovery.

The Spermine Oxidase/Spermine Axis Coordinates ATG5-Mediated Autophagy to Orchestrate Renal Senescence and Fibrosis

Decreased plasma spermine levels are associated with kidney dysfunction. However, the role of spermine in kidney disease remains largely unknown. Herein, it is demonstrated that spermine oxidase (SMOX), a key enzyme governing polyamine metabolism, is predominantly induced in tubular epithelium of human and mouse fibrotic kidneys, alongside a reduction in renal spermine content in mice. Moreover, renal SMOX expression is positively correlated with kidney fibrosis and function decline in patients with chronic kidney disease. Importantly, supplementation with exogenous spermine or genetically deficient SMOX markedly improves autophagy, reduces senescence, and attenuates fibrosis in mouse kidneys. Further, downregulation of ATG5, a critical component of autophagy, in tubular epithelial cells enhances SMOX expression and reduces spermine in TGF-β1-induced fibrogenesis in vitro and kidney fibrosis in vivo. Mechanically, ATG5 readily interacts with SMOX under physiological conditions and in TGF-β1-induced fibrogenic responses to preserve cellular spermine levels. Collectively, the findings suggest SMOX/spermine axis is a potential novel therapy to antagonize renal fibrosis, possibly by coordinating autophagy and suppressing senescence.

The role of polyamine metabolism in cellular function and physiology

Polyamines are molecules with multiple amino groups that are essential for cellular function. The major polyamines are putrescine, spermidine, spermine, and cadaverine. Polyamines are important for posttranscriptional regulation, autophagy, programmed cell death, proliferation, redox homeostasis, and ion channel function. Their levels are tightly controlled. High levels of polyamines are associated with proliferative pathologies such as cancer, whereas low polyamine levels are observed in aging, and elevated polyamine turnover enhances oxidative stress. Polyamine metabolism is implicated in several pathophysiological processes in the nervous, immune, and cardiovascular systems. Currently, manipulating polyamine levels is under investigation as a potential preventive treatment for several pathologies, including aging, ischemia/reperfusion injury, pulmonary hypertension, and cancer. Although polyamines have been implicated in many intracellular mechanisms, our understanding of these processes remains incomplete and is a topic of ongoing investigation. Here, we discuss the regulation and cellular functions of polyamines, their role in physiology and pathology, and emphasize the current gaps in knowledge and potential future research directions.

Regulatory mechanisms of dopamine metabolism in a marine Meyerozyma guilliermondii GXDK6 under NaCl stress as revealed by integrative multi-omics analysis

Dopamine can be used to treat depression, myocardial infarction, and other diseases. However, few reports are available on the de novo microbial synthesis of dopamine from low-cost substrate. In this study, integrated omics technology was used to explore the dopamine metabolism of a novel marine multi-stress-tolerant aromatic yeast Meyerozyma guilliermondii GXDK6. GXDK6 was found to have the ability to biosynthesize dopamine when using glucose as the substrate. 14 key genes for the biosynthesis of dopamine were identified by whole genome-wide analysis. Transcriptomic and proteomic data showed that the expression levels of gene AAT2 encoding aspartate aminotransferase (regulating dopamine anabolism) were upregulated, while gene AO-I encoding copper amine oxidase (involved in dopamine catabolism) were downregulated under 10 % NaCl stress compared with non-NaCl stress, thereby contributing to biosynthesis of dopamine. Further, the amount of dopamine under 10 % NaCl stress was 2.51-fold higher than that of zero NaCl, which was consistent with the multi-omics results. Real-time fluorescence quantitative PCR (RT-qPCR) and high-performance liquid chromatography (HPLC) results confirmed the metabolic model of dopamine. Furthermore, by overexpressing AAT2, AST enzyme activity was increased by 24.89 %, the expression of genes related to dopamine metabolism was enhanced, and dopamine production was increased by 56.36 % in recombinant GXDK6AAT2. In conclusion, Meyerozyma guilliermondii GXDK6 could utilize low-cost carbon source to synthesize dopamine, and NaCl stress promoted the biosynthesis of dopamine.

Inflammation primes the kidney for recovery by activating AZIN1 A-to-I editing

The progression of kidney disease varies among individuals, but a general methodology to quantify disease timelines is lacking. Particularly challenging is the task of determining the potential for recovery from acute kidney injury following various insults. Here, we report that quantitation of post-transcriptional adenosine-to-inosine (A-to-I) RNA editing offers a distinct genome-wide signature, enabling the delineation of disease trajectories in the kidney. A well-defined murine model of endotoxemia permitted the identification of the origin and extent of A-to-I editing, along with temporally discrete signatures of double-stranded RNA stress and Adenosine Deaminase isoform switching. We found that A-to-I editing of Antizyme Inhibitor 1 (AZIN1), a positive regulator of polyamine biosynthesis, serves as a particularly useful temporal landmark during endotoxemia. Our data indicate that AZIN1 A-to-I editing, triggered by preceding inflammation, primes the kidney and activates endogenous recovery mechanisms. By comparing genetically modified human cell lines and mice locked in either A-to-I edited or uneditable states, we uncovered that AZIN1 A-to-I editing not only enhances polyamine biosynthesis but also engages glycolysis and nicotinamide biosynthesis to drive the recovery phenotype. Our findings implicate that quantifying AZIN1 A-to-I editing could potentially identify individuals who have transitioned to an endogenous recovery phase. This phase would reflect their past inflammation and indicate their potential for future recovery.

Maybe the various forms of kidney disease are not so mechanistically different?

Sieckmann and colleagues provide evidence of a common abnormality in polyamine metabolism in 11 different rodent models of acute kidney injury and chronic kidney disease, and in human renal transplantation. The abnormality is characterized by downregulation of enzymes involved in polyamine synthesis and/or upregulation of enzymes involved in polyamine metabolism. Therefore, polyamine metabolism is a potential target for development of pharmacotherapies for a broad range of kidney diseases.