Identifying the molecular mechanisms of sepsis-associated acute kidney injury and predicting potential drugs

Efficacy of exosomes in acute kidney injury treatment and the associated mechanism (Review)

Acute kidney injury (AKI) is a syndrome characterized by rapid loss of renal function with a high morbidity and mortality. However, due to the complex pathophysiologic mechanisms of AKI, no specific treatment for this disease is currently available. Animal models have demonstrated the protective effects of exosomes on AKI; however, the underlying mechanisms require further investigation. The present review focuses on the efficacy of exosomes derived from different cell sources, including mesenchymal stem cells, endothelial progenitor cells and tubular epithelial cells, in the treatment of AKI and the associated mechanism. Furthermore, the effects of exosomal contents, including microRNAs, circular RNAs, long non‑coding RNAs, messenger RNAs and proteins, on the repair of renal tubules, protection against renal tubular epithelial cell injury, protection against fibrosis, inhibition of early endoplasmic reticulum stress and mediation of inflammation during AKI are also summarized in the present review.

LncRNA FENDRR/ miR-424-5p serves as a diagnostic biomarker for sepsis and its predictive value for clinical outcomes

PURPOSE

This study intends to investigate the relationship between FENDRR and miR-424-5p and their clinical significance in sepsis, aiming to provide new diagnostic markers and prognostic markers for sepsis.

METHODS

136 patients with sepsis and 132 healthy volunteers were included as study subjects. The expression levels of FENDRR and miR-424-5p were detected by qPCR. ROC was applied to evaluate the diagnostic value of FENDRR and miR-424-5p. COX analyzed the independent risk factors for the occurrence of death in sepsis patients. Dual luciferase reporter assay detected the binding of FENDRR and miR-424-5p. The miR-424-5p target genes were predicted and enriched for GO function and KEGG pathway.

RESULTS

FENDRR was up-regulated and miR-424-5p was down-regulated in patients with sepsis. FENDRR can target and bind to miR-424-5p. Both FENDRR and miR-424-5p showed significant diagnostic potential in sepsis and their combination significantly improved the diagnostic efficiency. FENDRR/miR-424-5p were significantly correlated with WBC, CRP, APACH II, and SOFA of sepsis patients. FENDRR and miR-424-5p were independent risk factors for mortality in sepsis patients. Sepsis patients with high FENDRR levels or low miR-424-5p levels had higher mortality. GO and KEGG enrichment analyses revealed that the targets of miR-424-5p were predominantly associated with cell functions and inflammatory signaling pathways.

CONCLUSION

Upregulated FENDRR and downregulated miR-424-5p expression can serve as biomarkers of sepsis with predictive value on the onset and prognostic outcome. FENDRR and miR-424-5p were correlated with the severity of sepsis and FENDRR can play a function in the sepsis progression via targeting miR-424-5p.

Revolutionizing the treatment of intervertebral disc degeneration: an approach based on molecular typing

BACKGROUND

Intervertebral disc degeneration (IVDD) is a significant cause of global disability, reducing labor productivity, increasing the burden on public health, and affecting socio-economic well-being. Currently, there is a lack of recognized clinical approaches for molecular classification and precision therapy.

METHODS

Chondrocyte differentiation and prognosis-related genes were extracted from single-cell RNA sequencing and multi-omics data in the Gene Expression Omnibus (GEO) database through chondrocyte trajectory analysis and non-parametric tests. Subsequently, a precise IVDD risk stratification system was developed using ConsensusClusterPlus analysis. The clinical significance of molecular typing was demonstrated through case-control trials involving IVDD patients. Specific inhibitors of molecular typing were predicted using the pRRophetic package in R language and then validated in vitro.

RESULTS

A stratified model for IVDD, considering chondrocyte differentiation and demonstrating high clinical relevance, was developed using a set of 44 chondrocyte fate genes. Extensive analyses of multi-omics data confirmed the clinical relevance of this model, indicating that cases in the High Chondrocyte Scoring Classification (HCSC) group had the most favorable prognosis, whereas those in the Low Chondrocyte Scoring Classification (LCSC) group had the worst prognosis. Additionally, clinical case-control studies provided evidence of the utility of IVDD molecular typing in translational medicine. A gene expression-based molecular typing approach was used to create a matrix identifying potential inhibitors specific to each IVDD subtype. In vitro experiments revealed that gefitinib, a drug designed for LCSC, not only had protective effects on chondrocytes but also could induce the conversion of LCSC into the HCSC subgroup. Therefore, IVDD molecular typing played a critical role in assisting clinicians with risk stratification and enabling personalized treatment decisions.

CONCLUSION

The results of the study have provided a comprehensive and clinically relevant molecular typing for IVDD, involving a precise stratification system that offers a new opportunity for customizing personalized treatments for IVDD.

The role of ferroptosis in acute kidney injury: mechanisms and potential therapeutic targets

Acute kidney injury (AKI) is one of the most common and severe clinical renal syndromes with high morbidity and mortality. Ferroptosis is a form of programmed cell death (PCD), is characterized by iron overload, reactive oxygen species accumulation, and lipid peroxidation. As ferroptosis has been increasingly studied in recent years, it is closely associated with the pathophysiological process of AKI and provides a target for the treatment of AKI. This review offers a comprehensive overview of the regulatory mechanisms of ferroptosis, summarizes its role in various AKI models, and explores its interaction with other forms of cell death, it also presents research on ferroptosis in AKI progression to other diseases. Additionally, the review highlights methods for detecting and assessing AKI through the lens of ferroptosis and describes potential inhibitors of ferroptosis for AKI treatment. Finally, the review presents a perspective on the future of clinical AKI treatment, aiming to stimulate further research on ferroptosis in AKI.

Ccl5+ Macrophages drive pro-inflammatory responses and neutrophil recruitment in sepsis-associated acute kidney injury

Sepsis leads to dysfunctional immune responses with multi-organ damage, and acute kidney injury (AKI) is a common complication of sepsis. To gain a deeper understanding of the specific underlying mechanisms of sepsis, we investigated the effects of specific macrophages on sepsis. To gain a deeper understanding of the specific underlying mechanisms of sepsis, we investigated the effects of specific macrophages on sepsis. Single-cell sequencing of a mouse model of endotoxemia revealed that sepsis is a common complication of sepsis. Single-cell sequencing of a mouse model of endotoxemia revealed that the emerging macrophage subpopulation Ccl5+ Mac was significantly pro-inflammatory, activating a large number of pathways activating a large number of pathways associated with immune response and inflammatory response, including IL6-JAK-STAT3 signaling, TGF-β signaling, and inflammatory response. Interestingly, we found that Ccl5+ Mac recruits neutrophil through CCL5-CCR1 ligand receptor pairs by cellular communication analysis thereby further affecting sepsis. We therefore hypothesize that this macrophage subpopulation is actively involved in the underlying molecular mechanisms of AKI. We therefore hypothesize that this macrophage subpopulation is actively involved in the underlying molecular mechanisms of AKI in sepsis and provide valuable insights.

Identification of immune-related mitochondrial metabolic disorder genes in septic shock using bioinformatics and machine learning

PURPOSE

Mitochondria are involved in septic shock and inflammatory response syndrome, which severely affects the life security of patients. It is necessary to recognize and explore the immune-mitochondrial genes in septic shock.

METHODS

The GSE57065 dataset was acquired from the Gene Expression Omnibus (GEO) database and filtered by limma and the weighted correlation network analysis (WGCNA) to identify mitochondrial-related differentially expressed genes (MitoDEGs) in septic shock. The function of MitoDEGs was analyzed using the Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA), respectively. The Protein-Protein Interaction (PPI) network composed of MitoDEGs was established using Cytoscape. Support Vector Machine Recursive Feature Elimination (SVM-RFE), Random Forest (RF), and Least Absolute Shrinkage and Selection Operator (LASSO) were used to identify diagnostic MitoDEGs, which were validated using receiver operating characteristic (ROC) analysis and Quantitative Real-time Reverse Transcription Polymerase Chain Reaction (qRT-PCR). Furthermore, the infiltration of immunocytes was analyzed using CIBERSORT, and the correlation between diagnostic MitoDEGs and immunocytes was explored using Spearman.

RESULTS

A total of 44 MitoDEGs were filtered, and functional enrichment analysis showed they were associated with mitochondrial function, and the PPI network had 457 nodes and 547 edges. Four diagnostic genes, MitoDEGs, PGS1, C6orf136, THEM4, and EPHX2, were identified by three machine learning algorithms, and qRT-PCR results obtained similar expression levels as bioinformatics analysis. Furthermore, the diagnostic model constructed by the diagnostic genes had fine diagnostic efficacy. Immunocyte infiltration analysis showed that activated immunocytes were abundant and correlated with hub genes, with neutrophils accounting for the largest proportion in septic shock.

CONCLUSIONS

In this study, we recognized four immune-mitochondrial key genes (PGS1, C6orf136, THEM4, and EPHX2) in septic shock and designed a novel gene diagnosis model that provided a new and meaningful way for the diagnosis of septic shock.

Human Umbilical Cord-Derived Mesenchymal Stem Cells-Exosomes-Delivered miR-375 Targets HDAC4 to Promote Autophagy and Suppress T Cell Apoptosis in Sepsis-Associated Acute Kidney Injury

This study sought to elucidate the mechanism of human umbilical cord-derived mesenchymal stem cells (HUCMSCs)-exosomes (Exos) in sepsis-associated acute kidney injury (SAKI). Exos were isolated from HUCMSCs and co-cultured with CD4+ T cells exposed to lipopolysaccharide to detect the effects of HUCMSCs-Exos on CD4+ T cell apoptosis and autophagy. miR-375 expression in CD4+ T cells and HUCMSCs-Exos was examined. The relationship between miR-375 and HDAC4 was analyzed. A mouse model of SAKI was established and injected with HUCMSCs-Exos to verify the function of HUCMSCs-Exos in vivo. HUCMSCs-Exos inhibited lipopolysaccharide-induced apoptosis of CD4+ T cells and promoted autophagy. miR-375 expression was noted to be elevated in the HUCMSCs-Exos. Importantly, HUCMSCs-Exos could deliver miR-375 into CD4+ T cells where miR-375 targeted HDAC4 and negatively regulated its expression. By this mechanism, HUCMSCs-Exos decreased CD4+ T cell apoptosis and augmented autophagy. This finding was further confirmed in an in vivo SAKI model. Collectively, HUCMSCs-Exos can protect against SAKI via delivering miR-375 that promotes autophagy and arrests T cell apoptosis through HDAC4 downregulation. These findings suggest a promising therapeutic potential for HUCMSCs-Exos in the context of SAKI.

Systems Approaches to Cell Culture-Derived Extracellular Vesicles for Acute Kidney Injury Therapy: Prospects and Challenges

Acute kidney injury (AKI) is a heterogeneous syndrome, comprising diverse etiologies of kidney insults that result in high mortality and morbidity if not well managed. Although great efforts have been made to investigate underlying pathogenic mechanisms of AKI, there are limited therapeutic strategies available. Extracellular vesicles (EV) are membrane-bound vesicles secreted by various cell types, which can serve as cell-free therapy through transfer of bioactive molecules. In this review, we first overview the AKI syndrome and EV biology, with a particular focus on the technical aspects and therapeutic application of cell culture-derived EVs. Second, we illustrate how multi-omic approaches to EV miRNA, protein, and genomic cargo analysis can yield new insights into their mechanisms of action and address unresolved questions in the field. We then summarize major experimental evidence regarding the therapeutic potential of EVs in AKI, which we subdivide into stem cell and non-stem cell-derived EVs. Finally, we highlight the challenges and opportunities related to the clinical translation of animal studies into human patients.

The impact of Bayesian optimization on feature selection

Feature selection is an indispensable step for the analysis of high-dimensional molecular data. Despite its importance, consensus is lacking on how to choose the most appropriate feature selection methods, especially when the performance of the feature selection methods itself depends on hyper-parameters. Bayesian optimization has demonstrated its advantages in automatically configuring the settings of hyper-parameters for various models. However, it remains unclear whether Bayesian optimization can benefit feature selection methods. In this research, we conducted extensive simulation studies to compare the performance of various feature selection methods, with a particular focus on the impact of Bayesian optimization on those where hyper-parameters tuning is needed. We further utilized the gene expression data obtained from the Alzheimer's Disease Neuroimaging Initiative to predict various brain imaging-related phenotypes, where various feature selection methods were employed to mine the data. We found through simulation studies that feature selection methods with hyper-parameters tuned using Bayesian optimization often yield better recall rates, and the analysis of transcriptomic data further revealed that Bayesian optimization-guided feature selection can improve the accuracy of disease risk prediction models. In conclusion, Bayesian optimization can facilitate feature selection methods when hyper-parameter tuning is needed and has the potential to substantially benefit downstream tasks.

Low-dose Olaparib improves septic cardiac function by reducing ferroptosis via accelerated mitophagy flux

Sepsis is a dysregulated response to infection that can result in life-threatening organ failure, and septic cardiomyopathy is a serious complication involving ferroptosis. Olaparib, a classic targeted drug used in oncology, has demonstrated potential protective effects against sepsis. However, the exact mechanisms underlying its action remain to be elucidated. In our study, we meticulously screened ferroptosis genes associated with sepsis, and conducted comprehensive functional enrichment analyses to delineate the relationship between ferroptosis and mitochondrial damage. Eight sepsis-characterized ferroptosis genes were identified in sepsis patients, including DPP4, LPIN1, PGD, HP, MAPK14, POR, GCLM, and SLC38A1, which were significantly correlated with mitochondrial quality imbalance. Utilizing DrugBank and molecular docking, we demonstrated a robust interaction of Olaparib with these genes. Lipopolysaccharide (LPS)-stimulated HL-1 cells and monocytes were used to establish an in vitro sepsis model. Additionally, an in vivo model was developed using mice subjected to cecal ligation and perforation (CLP). Intriguingly, low-dose Olaparib (5 mg/kg) effectively targeted and mitigated markers associated with ferroptosis, concurrently improving mitochondrial quality. This led to a marked enhancement in cardiac function and a significant increase in survival rates in septic mice (p < 0.05). The mechanism through which Olaparib ameliorates ferroptosis in cardiac and leukocyte cells post-sepsis is attributed to its facilitation of mitophagy, thus favoring mitochondrial integrity. In conclusion, our findings suggest that low-dose Olaparib can improve mitochondrial quality by accelerating mitophagy flux, consequently inhibiting ferroptosis and preserving cardiac function after sepsis.

Molecular Mechanisms of Ferroptosis and Their Involvement in Acute Kidney Injury

Ferroptosis is a novel way of regulating cell death, which occurs in a process that is closely linked to intracellular iron metabolism, lipid metabolism, amino acid metabolism, and multiple signaling pathways. The latest research shows that ferroptosis plays a key role in the pathogenesis of acute kidney injury (AKI). Ferroptosis may be an important target for treating AKI caused by various reasons, such as ischemia-reperfusion injury, rhabdomyolysis syndrome, sepsis, and nephrotoxic drugs. This paper provides a review on the regulatory mechanisms of ferroptosis and its role in AKI, which may help to provide new research ideas for the treatment of AKI and future research.

Ferroptosis: A new mechanism of traditional Chinese medicine compounds for treating acute kidney injury

Acute kidney injury (AKI) is a major health concern owing to its high morbidity and mortality rates, to which there are no drugs or treatment methods, except for renal replacement therapy. Therefore, identifying novel therapeutic targets and drugs for treating AKI is urgent. Ferroptosis is an iron-dependent and lipid-peroxidation-driven regulatory form of cell death and is closely associated with the occurrence and development of AKI. Traditional Chinese medicine (TCM) has unique advantages in treating AKI due to its natural origin and efficacy. In this review, we summarize the mechanisms underlying ferroptosis and its role in AKI, and TCM compounds that play essential roles in the prevention and treatment of AKI by inhibiting ferroptosis. This review suggests ferroptosis as a potential therapeutic target for AKI, and that TCM compounds show broad prospects in the treatment of AKI by targeting ferroptosis.