Identification of potential ferroptosis-related biomarkers and a pharmacological compound in diabetic retinopathy based on machine learning and molecular docking

Integration of Bioinformatics and Machine Learning Strategies Identifies Ferroptosis and Immune Infiltration Signatures in Peri-Implantitis

Peri-implantitis (PI) is a chronic inflammatory disease that ultimately leads to the dysfunction and loss of implants with established osseointegration. Ferroptosis has been implicated in the progression of PI, but its precise mechanisms remain unclear. This study explores the molecular mechanisms of ferroptosis in the pathology of PI through bioinformatics, offering new insights into its diagnosis and treatment. The microarray datasets for PI (GSE33774 and GSE106090) were retrieved from the GEO database. The differentially expressed genes (DEGs) and ferroptosis-related genes (FRGs) were intersected to obtain PI-Ferr-DEGs. Using three machine learning algorithms, the Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine-Recursive Feature Elimination (SVM-RFE), and Boruta, we successfully identified the most crucial biomarkers. Additionally, these key biomarkers were validated using a verification dataset (GSE223924). Gene set enrichment analysis (GSEA) was also utilized to analyze the associated gene enrichment pathways. Moreover, immune cell infiltration analysis compared the differential immune cell profiles between PI and control samples. Also, we targeted biomarkers for drug prediction and conducted molecular docking analysis on drugs with potential development value. A total of 13 PI-Ferr-DEGs were recognized. Machine learning and validation confirmed toll-like receptor-4 (TLR4) and FMS-like tyrosine kinase 3 (FLT3) as ferroptosis biomarkers in PI. In addition, GSEA was significantly enriched by the biomarkers in the cytokine-cytokine receptor interaction and chemokine signaling pathway. Immune infiltration analysis revealed that the levels of B cells, M1 macrophages, and natural killer cells differed significantly in PI. Ibudilast and fedratinib were predicted as potential drugs for PI that target TLR4 and FLT3, respectively. Finally, the occurrence of ferroptosis and the expression of the identified key markers in gingival fibroblasts under inflammatory conditions were validated by RT-qPCR and immunofluorescence analysis. This study identified TLR4 and FLT3 as ferroptosis and immune cell infiltration signatures in PI, unraveling potential novel targets to treat PI.

Identification of Key Nucleotide Metabolism Genes in Diabetic Retinopathy Based on Bioinformatics Analysis and Experimental Verification

A dysregulated nucleotide metabolism has been implicated in the pathogenesis of diabetic retinopathy (DR). RNA sequencing datasets, GSE102485, GSE60436, and GSE165784, were downloaded from the GEO database. The differentially expressed genes (DEGs) between the DR and controls overlapped with nucleotide metabolism-related genes (NM-RGs), resulting in the differentially expressed NM-RGs (DE-NMRGs). Next, the core genes were identified by the five algorithms of the CytoHubba plugin. Receiver Operating Characteristic (ROC) curves and gene expression analysis were utilized to confirm the biomarkers. Then, the correlations between biomarker expression and the immune-related module were analyzed. The miRNA and transcription factor (TF) predictions, biomarker-targeting drugs, and molecular docking were implemented separately. The interaction between each subcluster of DR was elucidated through single-cell RNA (scRNA) analysis. Moreover, RT-PCR was applied to verify the expression of the biomarkers. In GSE102485, 48 DE-NMRGs were identified via the intersection of 1359 DEGs and 882 NM-RGs. Using the CytoHubba plugin, HMOX1, TLR4, and ACE were selected as core genes. As per the GSVA result, the interferon alpha response, IL6_JAK_STAT3 signaling, and apoptosis were activated in the DR group. The TF prediction identified TLR4 and HMOX1 as potential target genes of USF2. In conclusion, ACE and HMOX1 were possible diagnostic biomarkers related to nucleotide metabolism in DR.

Resveratrol Protects Müller Cells Against Ferroptosis in the Early Stage of Diabetic Retinopathy by Regulating the Nrf2/GPx4/PTGS2 Pathway

The aim of this study was to investigate the anti-ferroptotic effect of resveratrol (RSV) on retinal Müller cells (RMCs) in the early stages of diabetic retinopathy (DR) via the nuclear factor erythroid 2-related factor 2 (Nrf2)/glutathione peroxidase 4 (GPx4)/prostaglandin-endoperoxide synthase 2 (PTGS2). The retina was obtained from normal and diabetic Sprague-Dawley rats or wild-type and Nrf2 knockout (KO) diabetic mice, with or without RSV (10 mg/kg/d) treatment for 12 weeks. RMCs transfected with or without SiNrf2 were cultured with high glucose and RSV (20 mM). The retinal neurofunctional changes were measured by electroretinogram (ERG). The retinal inner nuclear layer cell mitochondrial morphological changes were detected by transmission electron microscopy. The cell viabilities were measured by cell counting kit-8 (CCK-8) assay. The levels of Fe2+, malonic dialdehyde (MDA), and glutathione (GSH) were measured by colorimetric method. The expression of Nrf2, GPx4, and PTGS2 was detected by quantitative real-time polymerase chain reaction (qRT-PCR), western blotting, and immunocytochemistry. In vivo, RSV inhibited retinal neurofunctional changes and mitochondrial morphological changes; decreased Fe2+, MDA, and PTGS2; and increased GSH, Nrf2, and GPx4 in retina of DM rats. In vitro, RSV decreased MDA and PTGS2 and increased cell viability, GSH, Nrf2, and GPx4. In vivo and vitro, the role of Nrf2-regulated signaling pathway in anti-ferroptosis by RSV was further confirmed using Nrf2 KO mice and pre-transfected SiNrf2 in RMCs. These findings indicated that RSV is a potential therapeutic option for DR and that Nrf2/GPx4/PTGS2 plays a role in the anti-ferroptosis mechanism of RSV on RMCs.

Autophagy-dependent ferroptosis may play a critical role in early stages of diabetic retinopathy

Diabetic retinopathy (DR), as one of the most common and significant microvascular complications of diabetes mellitus (DM), continues to elude effective targeted treatment for vision loss despite ongoing enrichment of the understanding of its pathogenic mechanisms from perspectives such as inflammation and oxidative stress. Recent studies have indicated that characteristic neuroglial degeneration induced by DM occurs before the onset of apparent microvascular lesions. In order to comprehensively grasp the early-stage pathological changes of DR, the retinal neurovascular unit (NVU) will become a crucial focal point for future research into the occurrence and progression of DR. Based on existing evidence, ferroptosis, a form of cell death regulated by processes like ferritinophagy and chaperone-mediated autophagy, mediates apoptosis in retinal NVU components, including pericytes and ganglion cells. Autophagy-dependent ferroptosis-related factors, including BECN1 and FABP4, may serve as both biomarkers for DR occurrence and development and potentially crucial targets for future effective DR treatments. The aforementioned findings present novel perspectives for comprehending the mechanisms underlying the early-stage pathological alterations in DR and open up innovative avenues for investigating supplementary therapeutic strategies.

A New Modulator of Neuroinflammation in Diabetic Retinopathy: USP25

Diabetic retinopathy (DR) is a diabetes-associated complication that poses a threat to vision, distinguished by persistent and mild inflammation of the retinal microvasculature. The activation of microglia plays a crucial role in driving this pathological progression. Previous investigations have demonstrated that ubiquitin-specific peptidase 25 (USP25), a deubiquitinating enzyme, is involved in the regulation of immune cell activity. Nevertheless, the precise mechanisms through which USP25 contributes to the development of DR remain incompletely elucidated. Firstly, we have demonstrated the potential mechanism by which ROCKs can facilitate microglial activation and augment the synthesis of inflammatory mediators through the modulation of NF-κB signaling pathways in a high-glucose milieu. Furthermore, our study has provided novel insights by demonstrating that the regulatory role of USP25 in the secretion of proinflammatory factors is mediated through the involvement of ROCK in modulating the expression of NF-κB and facilitating the nuclear translocation of the phosphatase NF-κB. This regulatory mechanism plays a crucial role in modulating the activation of microglial cells within a high-glycemic environment. Hence, USP25 emerges as a pivotal determinant for the inflammatory activation of microglial cells, and its inhibition exhibits a dual effect of promoting retinal neuron survival while suppressing the inflammatory response in the retina. In conclusion, the promotion of diabetic retinopathy (DR) progression by USP25 is attributed to its facilitation of microglial activation induced by high glucose levels, a process mediated by the ROCK pathway. These findings highlight the importance of considering USP25 as a potential therapeutic target for the management of diabetic neuroinflammation.

Non-Apoptotic Programmed Cell Death as Targets for Diabetic Retinal Neurodegeneration

Diabetic retinopathy (DR) remains the leading cause of blindness among the global working-age population. Emerging evidence underscores the significance of diabetic retinal neurodegeneration (DRN) as a pivotal biomarker in the progression of vasculopathy. Inflammation, oxidative stress, neural cell death, and the reduction in neurotrophic factors are the key determinants in the pathophysiology of DRN. Non-apoptotic programmed cell death (PCD) plays a crucial role in regulating stress response, inflammation, and disease management. Therapeutic modalities targeting PCD have shown promising potential for mitigating DRN. In this review, we highlight recent advances in identifying the role of various PCD types in DRN, with specific emphasis on necroptosis, pyroptosis, ferroptosis, parthanatos, and the more recently characterized PANoptosis. In addition, the therapeutic agents aimed at the regulation of PCD for addressing DRN are discussed.

Epigenetic mechanism of SET7/9-mediated histone methylation modification in high glucose-induced ferroptosis in retinal pigment epithelial cells

Ferroptosis of the retinal pigment epithelial (RPE) cells leads to retinal neuron injury and even visual loss. Our study aims to investigate the role of the SET domain with lysine methyltransferase 7/9 (SET7/9) in regulating high glucose (HG)-induced ferroptosis in RPE cells. The cell model was established by HG treatment. The levels of SET7/9 and Sirtuin 6 (SIRT6) were inhibited and Runt-related transcription factor 1 (RUNX1) was overexpressed through cell transfection, and then their levels in ARPE-19 cells were detected. Cell viability and apoptosis was detected. The levels of reactive oxygen species, malondialdehyde, glutathione, ferrous ion, glutathione peroxidase 4, and acyl-CoA synthetase long-chain family member 4 were detected. SET7/9 and trimethylation of histone H3 at lysine 4 (H3K4me3) levels in the RUNX1 promoter region and RUNX1 level in the SIRT6 promoter region were measured. The relationship between RUNX1 and SIRT6 was verified. SET7/9 and RUNX1 were highly expressed while SIRT6 was poorly expressed in HG-induced ARPE-19 cells. SET7/9 inhibition increased cell viability and inhibited cell apoptosis and ferroptosis. Mechanistically, SET7/9 increased H3K4me3 on the RUNX1 promoter to promote RUNX1, and RUNX1 repressed SIRT6 expression. Overexpression of RUNX1 or silencing SIRT6 partially reversed the inhibitory effect of SET7/9 silencing on HG-induced ferroptosis. In conclusion, SET7/9 promoted ferroptosis of RPE cells through the SIRT6/RUNX1 pathway.

Identification of biomarkers associated with ferroptosis in diabetic retinopathy based on WGCNA and machine learning

Objective: Diabetic retinopathy (DR) is a chronic progressive eye disease that affects millions of diabetic patients worldwide, and ferroptosis may contribute to the underlying mechanisms of DR. The main objective of this work is to explore key genes associated with ferroptosis in DR and to determine their feasibility as diagnostic markers. Methods: WGCNA identify the most relevant signature modules in DR. Machine learning methods were used to de-screen the feature genes. ssGSEA calculated the scoring of immune cells in the DR versus control samples and compared the associations with the core genes by Spearman correlation. Results: We identified 2,897 differential genes in DR versus normal samples. WGCNA found tan module to have the highest correlation with DR patients. Finally, 20 intersecting genes were obtained from differential genes, tan module and iron death genes, which were screened by LASSO and SVM-RFE method, and together identified 6 genes as potential diagnostic markers. qPCR verified the expression and ROC curves confirmed the diagnostic accuracy of the 6 genes. In addition, our ssGSEA scoring identified these 6 core genes as closely associated with immune infiltrating cells. Conclusion: In conclusion, we analyzed for the first time the potential link of iron death in the pathogenesis of DR. This has important implications for future studies of iron death-mediated pro-inflammatory immune mechanisms.

The effect evaluation of continuous nursing intervention in patients with type 2 diabetic retinopathy

INTRODUCTION

To evaluate the application effect of continuous nursing intervention in type 2 diabetic retinopathy (DR).

METHODS

Patients with type 2 DR were selected and divided into intervention group and control group by random. The control group received routine nursing intervention, and the intervention group received continuous nursing intervention on the basis of the control group. The clinical effects of the two groups were compared.

RESULTS

After 1 and 2 years of intervention, the intervention group compared to the control group. The rate of visual acuity decrease was significantly lower (p < 0.05). Fasting blood glucose, 2 h postprandial blood glucose, and glycosylated hemoglobin were significantly lower (p < 0.05). The self-management ability and satisfaction were significantly higher, and the readmission rate was significantly lower (p < 0.05).

CONCLUSION

The continuous nursing intervention model has a good clinical effect on the visual acuity of patients with type 2 DR.

Comprehensive analysis of ferritinophagy-related genes and immune infiltration landscape in diabetic retinopathy

Background

Diabetic retinopathy (DR) is deemed a microangiopathy and neurodegenerative disorder, which is a primary reason of visual impairment in the world. Ferritinophagy is a critical regulator of ferroptosis and has a vital part in the etiopathogenesis of DR. Nevertheless, its molecular mechanism in DR remains to be expounded.

Methods

The GSE146615 dataset was adopted to identify ferritinophagy-related differentially expressed genes (FRDEGs). The interactions and biological functions of the genes were described by means of functional enrichment analysis (FEA). The enriched gene sets were analyzed utilizing gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA). Identification of hub genes was performed utilizing protein-protein interaction (PPI) analysis. mRNA-miRNA, mRNA-transcription factors (TF), mRNA-drugs, mRNA-RNA-binding proteins (RBP) interaction networks were constructed. In addition, datasets GSE60436 and GSE94019 were utilized for validation. The diagnostic performance of FRDEGs was assessed by means of receiver-operating characteristic curve monofactor analysis, followed by immune infiltration analysis. Lastly, quantitative real-time polymerase chain reaction (qRT-PCR) was implemented to analyze the validation of genes.

Results

In total, the identification of eight FRDEGs was completed utilizing differential expression analysis. FEA mainly implicated the autophagy of mitochondrion, mitochondrion disassembly, autophagosome assembly, and organization pathways. GSEA and GSVA mainly implicated the interferon alpha response, ultraviolet response up, interferon gamma response, apical junction, pical surface, and allograft rejection pathways. BECN1 and HERC2 displayed high diagnostic accuracies in validation sets. Immune infiltration analysis revealed that several immune cells related to ferritinophagy may be play potential roles in DR. Finally, qRT-PCR was utilized to validate the upregulated expression of BECN1 as well as the downregulated expression of BCAT2 and ATG7 in the DR model.

Conclusion

BECN1, HERC2, ATG7, and BCAT2 act as potential biomarkers for DR and might regulate ferritinophagy and the immune microenvironment to influence its development and progression. This research can provide new insights into pathogenesis of DR related to ferritinophagy.