Identification of driver genes in lupus nephritis based on comprehensive bioinformatics and machine learning

A potential XGBoost Diagnostic Score for Staphylococcus aureus bloodstream infection

Staphylococcus aureus (S. aureus) bloodstream infection is often life-threatening, and increasing in incidence. We identified 63 differentially expressed genes (DEGs) in the GSE33341 S. aureus infection samples. Subsequently, intersecting the 63 DEGs with 950 genes from the blue module through weighted gene co-expression network analysis (WGCNA) yielded 38 genes. We leveraged Boruta and least absolute shrinkage and selection operator (LASSO) algorithms and identified5 diagnostic genes (DRAM1, UPP1, IL18RAP, CLEC4A, and PGLYRP1). Comparative analysis revealed that Extreme Gradient Boosting (XGBoost) surpassed SVM-RFE and Random Forest models, demonstrating superior diagnostic performance for S. aureus bloodstream infection (mean AUC for XGBoost =0.954; mean AUC for SVM-RFE =0.93275; mean AUC for Random Forest =0.94625). The XGBoost Diagnostic Score correlated with multiple immune cells to varying degrees, manifesting significant negative associations with CD8 T cells and CD4 naive T cells in both human and mouse samples. The diagnostic power of the Diagnostic Score was further validated by RT-qPCR results obtained from both mouse and patient samples, as well as RNA-Seq analysis conducted on mouse samples. XGBoost Diagnostic Score, consisting of DRAM1, UPP1, IL18RAP, CLEC4A, and PGLYRP1, may serve as a Diagnostic tool for S. aureus bloodstream infection.

Macrophage polarization regulates the pathogenesis and progression of autoimmune diseases

Macrophages are integral components of the innate immune system, present in nearly all tissues and organs throughout the body. They exhibit a high degree of plasticity and heterogeneity, participating in immune responses to maintain immune homeostasis. When the immune system loses tolerance, macrophages rapidly proliferate and polarize in response to various signaling pathways within a disrupted microenvironment. The direction of macrophage polarization can be regulated by a variety of factors, including transcription factors, non-coding RNAs, and metabolic reprogramming. Autoimmune diseases arise from the immune system's activation against host cells, with macrophage polarization playing a critical role in the pathogenesis of numerous chronic inflammatory and autoimmune conditions, such as rheumatoid arthritis, systemic lupus erythematosus, immune thrombocytopenic purpura, and type 1 diabetes. Consequently, elucidating the molecular mechanisms underlying macrophage development and function presents opportunities for the development of novel therapeutic targets. This review outlines the functions of macrophage polarization in prevalent autoimmune diseases and the underlying mechanisms involved. Furthermore, we discuss the immunotherapeutic potential of targeting macrophage polarization and highlight the characteristics and recent advancements of promising therapeutic targets. Our aim is to inspire further strategies to restore macrophage balance in preventing and treating autoimmune diseases.

Identification of ALDH2 as a novel target for the treatment of acute kidney injury in kidney transplantation based on WGCNA and machine learning algorithms and exploration of its potential mechanism of action using animal experiments

Background

Acute kidney injury (AKI) after kidney transplantation is one of the main causes of graft loss and poor patient prognosis, and it is important to explore new targets for treating AKI in kidney transplantation.

Methods

Based on the kidney transplantation AKI-related dataset GSE30718, the most relevant modular genes for AKI among them were firstly screened using WGCNA and intersected with the DEGs, and the intersected genes were used as candidate genes for kidney transplantation AKI. Second, machine learning algorithms were utilized to identify the key genes among them, and the HPA database was used to explore the expression landscape. Next, we constructed a rat renal IRI model and explored the role of key genes in renal IRI. Finally, we combined ssGSEA enrichment analysis with animal experiments to further validate the potential mechanism of action of key genes.

Results

In total, we identified 98 of the most relevant modular genes for AKI and 417 DEGs, which intersected to yield a total of 24 AKI candidate genes. Next, we intersected the key genes identified by three types of machine learning, namely, Random Forest, LASSO regression analysis and SVM, and obtained a total of 1 intersected gene as ALDH2, which we used as a key gene in kidney transplantation AKI. Using the HPA database, we found that ALDH2 has a high expression level in renal tissues and is mainly located in renal tubular epithelial cells. Next, we found in a rat renal IRI model that increasing the expression of ALDH2 alleviated the impairment of renal function and decreased the expression of NGAL, a marker of tubular injury, and BAX, an apoptotic protein, as well as reducing the expression of the inflammatory factors IL1β and IL6. Finally, using ssGSEA enrichment analysis and animal experiments, we further found that ALDH2 was able to inhibit the activation of the MAPK signaling pathway.

Conclusion

ALDH2 may serve as a novel target for the treatment of kidney transplantation AKI, and increasing the expression level of ALDH2 has a protective effect on renal IRI, and this protective effect may be achieved by inhibiting the MAPK signaling pathway.

Screening, identification and targeted intervention of necroptotic biomarkers of asthma

BACKGROUND

As a pivotal pathway of programmed cell death, necroptosis significantly contributes to the pathogenesis of respiratory disorders. However, its role in asthma is not yet fully elucidated. Therefore, this study aimed to identify markers associated with necroptosis, evaluate their functions in asthma, and explore potential therapeutic agents targeting necroptosis for the management of asthma.

METHODS

Firstly, machine learning algorithms, including Least Absolute Shrinkage and Selection Operator (LASSO), Random Forest, and Support Vector Machine-Recursive Feature Elimination (SVM-RFE), were utilized to identify necroptosis-related differentially expressed genes (NRDEGs) in asthma patients compared to healthy controls. Concurrently, the expression of NRDEGs was validated using external datasets, Western blot, and quantitative real-time polymerase chain reaction (qPCR). Secondly, the clinical relevance of NRDEGs was assessed through Receiver Operating Characteristic (ROC) curve analysis and correlation with clinical indicators. Thirdly, the relationship between NRDEGs and pulmonary immune cell infiltration, as well as the signaling interactions between different cells types, were analyzed through immune infiltration and single-cell analysis. Fourthly, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA), were conducted to elucidate the functional roles of NRDEGs. Finally, compounds targeting NRDEGs were screened, and their binding affinities were evaluated using molecular docking studies.

RESULTS

In asthma, necroptosis is activated, leading to the identification of four NRDEGs: NLRP3, PYCARD, ALOX15, and VDAC3. Among these, NLRP3, PYCARD, and ALOX15 are upregulated, whereas VDAC3 is downregulated in asthma. Comprehensive clinical evaluations indicated that NRDEGs hold diagnostic value for asthma. Specifically, NLRP3 was inversely correlated with forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC), while VDAC3 showed an inverse correlation with sputum neutrophils. Conversely, ALOX15 expression was positively correlated with fractional exhaled nitric oxide (FeNO) levels, as well as sputum eosinophils, blood eosinophils, and blood IgE levels. Subsequent immune infiltration analysis revealed associations between NRDEGs and activated dendritic cells, mast cells, and eosinophils. Single-cell RNA sequencing (scRNA-seq) further confirmed the communication signals between myeloid dendritic cells, fibroblasts, neutrophils, and helper T cells, predominantly related to fibrosis and immune-inflammatory responses. Pathway enrichment analysis demonstrated that NRDEGs are involved in ribosomal function, oxidative phosphorylation, and fatty acid metabolism. Finally, resveratrol and triptonide were identified as potential therapeutic agents targeting the proteins encoded by NRDEGs for asthma treatment.

CONCLUSIONS

The necroptosis pathway is activated in asthma, with NRDEGs-namely PYCARD, NLRP3, ALOX15, and VDAC3-correlated with declines in lung function and airway inflammation. These genes serve as reliable predictors of asthma risk and are involved in the regulation of the immune-inflammatory microenvironment. Resveratrol and triptolide have been identified as promising therapeutic candidates due to their potential to target the proteins encoded by these genes.

LncRNA XIST/miR-381-3P/STAT1 axis as a potential biomarker for lupus nephritis

OBJECTIVE

We aim to investigate the potential roles of key genes in the development of lupus nephritis (LN), screen key biomarkers, and construct the lncRNA XIST/miR-381-3P/STAT1 axis by using bioinformatic prediction combined with clinical validation, thereby providing new targets and insights for clinical research.

METHODS

Gene expression microarrays GSE157293 and GSE112943 were downloaded from the GEO database to obtain differentially expressed genes (DEGs), followed by enrichment analyses on these DEGs, which were enriched and analyzed to construct a protein-protein interaction (PPI) network to screen core genes. The lncRNA-miRNA-mRNA regulatory network was predicted and constructed based on the miRNA database. 37 female patients with systemic lupus erythematosus (SLE) were recruited to validate the bioinformatics results by exploring the diagnostic value of the target ceRNA axis in LN by dual luciferase and real-time fluorescence quantitative PCR (RT-qPCR) and receiver operating characteristic (ROC).

RESULTS

The data represented that a total of 133 differential genes were screened in the GSE157293 dataset and 2869 differential genes in the GSE112943 dataset, yielding a total of 26 differentially co-expressed genes. Six core genes (STAT1, OAS2, OAS3, IFI44, DDX60, and IFI44L) were screened. Biological functional analysis identified key relevant pathways in LN. ROC curve analysis suggested that lncRNA XIST, miR-381-3P, and STAT1 could be used as potential molecular markers to assist in the diagnosis of LN.

CONCLUSION

STAT1 is a key gene in the development of LN. In conclusion, lncRNA XIST, miR-381-3P, and STAT1 can be used as new molecular markers to assist in the diagnosis of LN, and the lncRNA XIST/miR-381-3P/STAT1 axis may be a potential therapeutic target for LN.

Lupus Nephritis from Pathogenesis to New Therapies: An Update

Lupus Nephritis (LN) still represents one of the most severe complications of Systemic Lupus Erythematosus (SLE) and a major risk factor for morbidity and mortality. However, over the last few years, several studies have paved the way for a deeper understanding of its pathogenetic mechanisms and more targeted treatments. This review aims to provide a comprehensive update on progress on several key aspects in this setting: pathogenetic mechanisms of LN, including new insight into the role of autoantibodies, complement, vitamin D deficiency, and interaction between infiltrating immune cells and kidney resident ones; the evolving role of renal biopsy and biomarkers, which may integrate information from renal histology; newly approved drugs such as voclosporin (VOC) and belimumab (BEL), allowing a more articulate strategy for induction therapy, and other promising phase III-immunosuppressive (IS) agents in the pipeline. Several adjunctive treatments aimed at reducing cardiovascular risk and progression of chronic renal damage, such as antiproteinuric agents, represent an important complement to IS therapy. Furthermore, non-pharmacological measures concerning general lifestyle and diet should also be adopted when managing LN. Integrating these therapeutic areas requires an effort towards a holistic and multidisciplinary approach. At the same time, the availability of an increasingly wider armamentarium may translate into improvements in patient's renal outcomes over the next decades.

Lupus Nephritis Biomarkers: A Critical Review

Lupus nephritis (LN), a major complication in individuals diagnosed with systemic lupus erythematosus, substantially increases morbidity and mortality. Despite marked improvements in the survival of patients with severe LN over the past 50 years, complete clinical remission after immunosuppressive therapy is achieved in only half of the patients. Therefore, timely detection of LN is vital for initiating prompt therapeutic interventions and improving patient outcomes. Biomarkers have emerged as valuable tools for LN detection and monitoring; however, the complex role of these biomarkers in LN pathogenesis remains unclear. Renal biopsy remains the gold standard for the identification of the histological phenotypes of LN and guides disease management. However, the molecular pathophysiology of specific renal lesions remains poorly understood. In this review, we provide a critical, up-to-date overview of the latest developments in the field of LN biomarkers.