Identification of Ferroptotic Genes in Spinal Cord Injury at Different Time Points: Bioinformatics and Experimental Validation

Machine Learning and Experiments Revealed Key Genes Related to PANoptosis Linked to Drug Prediction and Immune Landscape in Spinal Cord Injury

Spinal cord injury (SCI) is a severe central nervous system injury without effective therapies. PANoptosis is involved in the development of many diseases, including brain and spinal cord injuries. However, the biological functions and molecular mechanisms of PANoptosis-related genes in spinal cord injury remain unclear. In the bioinformatics analysis of public data of SCI, the differentially expressed genes (DEGs) identified by GSE151371 were hybridized with PANoptosis-related genes (PRGs) to obtain differentially expressed PANoptosis-related genes (DE-PRGs). Through three machine learning algorithms, we obtained the hub genes. Then, we constructed functional analysis, drug prediction, regulatory network construction, and immune infiltrating cell analysis. Finally, the expression of the hub gene was verified in GSE93561, GSE45376, and qRT-PCR analysis. Through the above analysis, 14 DE-PRGs were obtained by intersecting 3582 DEGs with 46 PRGs. Five key hub genes, CASP4, GSDMB, NAIP, NLRC4, and NLRP3, were obtained by 3 machine learning algorithms. All five hub genes were enriched in phagocytosis mediated by FC GAMMA R. The 11 immune cells were significantly different between spinal cord injury (SCI) group and human control (HC) group, such as mast cell and gamma delta T cell. The transcription factor (TF)-hub gene network contained 10-nodes (4 hub genes and 6 TFs) and 8-edges. The miRNA-hub gene network consisting of 5-nodes (3 hub genes and 2 miRNAs) and 3-edges was constructed. Moreover, the CASP4 predicted 1 small molecule drug and NLRP3 predicted 9 small molecule drugs. Finally, the expression of 5 hub genes were significantly different in GSE45376 and GSE93561 (SCI vs. HC) and mice SCI model (Sham vs. SCI). Collectively, we identified 5 hub genes (CASP4, GSDMB, NAIP, NLRC4, and NLRP3) associated with PANoptosis, providing potential directions for treating spinal cord injury.

The Interplay Between Endoplasmic Reticulum Stress and Ferroptosis in Neurological Diseases

Many studies in the open literature have highlighted the critical roles of endoplasmic reticulum stress and ferroptosis in neurological diseases such as neurodegenerative diseases, brain injuries, and depression, indicating that they are involved in the onset and progression of these diseases. Therefore, it is essential to explore the regulatory mechanisms and potential interventions targeting endoplasmic reticulum stress and ferroptosis in neurological diseases. However, most existing research has primarily focused on the unidirectional mechanisms of endoplasmic reticulum stress and ferroptosis within the nervous system, with a lack of in-depth investigations into their interactions. In this paper, we first present an overview of the pathogenesis of endoplasmic reticulum stress and ferroptosis, along with their roles in neurological diseases. We then summarize the latest findings on the interaction mechanism between endoplasmic reticulum stress and ferroptosis from the perspectives of calcium iron homeostasis, reactive oxygen species, microenvironment, and related factors. Finally, we explore the potential molecular mechanisms and targeted interventions associated with endoplasmic reticulum stress and ferroptosis in neurological diseases.

PGK1 Is Involved in the HIF-1 Signaling Pathway as a Hub Gene for Ferroptosis After Traumatic Brain Injury

The pathogenesis of ferroptosis in traumatic brain injury (TBI) is unclear; therefore, we aimed to identify key molecules associated with ferroptosis in TBI using bioinformatics analysis to determine its underlying mechanisms. GSE128543 dataset was downloaded from the Gene Expression Omnibus (GEO) database, and TBI-associated modules were obtained by weighted gene co-expression network analysis (WGCNA). We identified 60 differentially expressed genes (DEGs) by intersecting the modules with ferroptosis and glycolysis/gluconeogenesis gene libraries. The hypoxia-inducible factor-1 (HIF-1) signaling pathway was identified to be critical for ferroptosis post-TBI, and protein-protein interaction (PPI) network identified 20 hub genes, including phosphoglycerate kinase 1 (PGK1), ribosomal protein (RP) family, pyruvate kinase M1/2 (PKM), hypoxia-inducible factor 1α subunit (HIF-1α), and MYC genes. In this study, we further explored the role of PGK1, a gene involved in HIF-1 signaling pathway; however, its role and mechanism in TBI are still unclear. Moreover, we constructed a TBI mouse model and examined PGK1 and HIF-1α expression levels, and the results revealed their expressions increased after cortical injury in mice and they co-localized in the same cells. Furthermore, we examined the expressions of PGK1 in the cerebrospinal fluid of 20 clinical patients with different degrees of brain injuries within 48 h of surgery and examined the cognitive function of patients according to the Glasgow Coma Scale (GCS). The results revealed that PGK1 expression level was negatively correlated with the severity of the brain injury. These findings suggest that PGK1 may become a potential hub gene for ferroptosis via the HIF-1 signaling pathway, second to neurological injury after TBI, thereby affecting patient prognosis.

CHAC1: a master regulator of oxidative stress and ferroptosis in human diseases and cancers

CHAC1, an essential regulator of oxidative stress and ferroptosis, is increasingly recognized for its significant roles in these cellular processes and its impact on various human diseases and cancers. This review aims to provide a comprehensive overview of CHAC1's molecular functions, regulatory mechanisms, and effects in different pathological contexts. Specifically, the study objectives are to elucidate the biochemical pathways involving CHAC1, explore its regulatory network, and discuss its implications in disease progression and potential therapeutic strategies. As a γ-glutamyl cyclotransferase, CHAC1 degrades glutathione, affecting calcium signaling and mitochondrial function. Its regulation involves transcription factors like ATF4 and ATF3, which control CHAC1 mRNA expression. CHAC1 is crucial for maintaining redox balance and regulating cell death pathways in cancer. Its elevated levels are associated with poor prognosis in many cancers, indicating its potential as a biomarker and therapeutic target. Additionally, CHAC1 influences non-cancerous diseases such as neurodegenerative and cardiovascular disorders. Therapeutically, targeting CHAC1 could increase cancer cell sensitivity to ferroptosis, aiding in overcoming resistance to standard treatments. This review compiles current knowledge and recent discoveries, emphasizing CHAC1's vital role in human diseases and its potential in diagnostic and therapeutic applications.

The potential roles of HIF-1α in epithelial-mesenchymal transition and ferroptosis in tumor cells

In tumors, the rapid proliferation of cells and the imperfect blood supply system lead to hypoxia, which can regulate the adaptation of tumor cells to the hypoxic environment through hypoxia-inducible factor-1α (HIF-1α) and promote tumor development in multiple ways. Recent studies have found that epithelial-mesenchymal transition (EMT) and ferroptosis play important roles in the progression of tumor cells. The activation of HIF-1α is considered a key factor in inducing EMT in tumor cells. When HIF-1α is activated, it can regulate EMT-related genes, causing tumor cells to gradually lose their epithelial characteristics and acquire more invasive mesenchymal traits. The occurrence of EMT allows tumor cells to better adapt to changes in the surrounding tissue, enhancing their migratory and invasive capabilities, thus promoting tumor progression. At the same time, HIF-1α also plays a crucial regulatory role in ferroptosis in tumor cells. In a hypoxic environment, HIF-1α may affect processes such as iron metabolism and oxidative stress responses, inducing ferroptosis in tumor cells. This article briefly reviews the dual role of HIF-1α in EMT and ferroptosis in tumor cells, helping to gain a deeper understanding of the regulatory pathways of HIF-1α in the development of tumor cells, providing a new perspective for understanding the pathogenesis of tumors. The regulation of HIF-1α may become an important strategy for future tumor therapy.

Metformin alleviates spinal cord injury by inhibiting nerve cell ferroptosis through upregulation of heme oxygenase-1 expression

JOURNAL/nrgr/04.03/01300535-202409000-00037/figure1/v/2024-01-16T170235Z/r/image-tiff Previous studies have reported upregulation of heme oxygenase-1 in different central nervous system injury models. Heme oxygenase-1 plays a critical anti-inflammatory role and is essential for regulating cellular redox homeostasis. Metformin is a classic drug used to treat type 2 diabetes that can inhibit ferroptosis. Previous studies have shown that, when used to treat cardiovascular and digestive system diseases, metformin can also upregulate heme oxygenase-1 expression. Therefore, we hypothesized that heme oxygenase-1 plays a significant role in mediating the beneficial effects of metformin on neuronal ferroptosis after spinal cord injury. To test this, we first performed a bioinformatics analysis based on the GEO database and found that heme oxygenase-1 was upregulated in the lesion of rats with spinal cord injury. Next, we confirmed this finding in a rat model of T9 spinal cord compression injury that exhibited spinal cord nerve cell ferroptosis. Continuous intraperitoneal injection of metformin for 14 days was found to both upregulate heme oxygenase-1 expression and reduce neuronal ferroptosis in rats with spinal cord injury. Subsequently, we used a lentivirus vector to knock down heme oxygenase-1 expression in the spinal cord, and found that this significantly reduced the effect of metformin on ferroptosis after spinal cord injury. Taken together, these findings suggest that metformin inhibits neuronal ferroptosis after spinal cord injury, and that this effect is partially dependent on upregulation of heme oxygenase-1.

ADSC-Exos enhance functional recovery after spinal cord injury by inhibiting ferroptosis and promoting the survival and function of endothelial cells through the NRF2/SLC7A11/GPX4 pathway

BACKGROUND

Spinal cord injury (SCI) is a devastating disease that causes major motor, sensory and autonomic dysfunctions. Currently, there is a lack of effective treatment. In this study, we aimed to investigate the potential mechanisms of Exosomes from adipose-derived stem cells (ADSC-Exos) in reducing ferroptosis and promoting angiogenesis after spinal cord injury.

METHODS

We isolated ADSC-Exos, the characteristics of which were confirmed. In vitro, we tested the potential of ADSC-Exos to promote the survival and function of human brain microvascular endothelial cells (HBMECs) and analyzed the ferroptosis of HBMECs. In vivo, we established rat models of SCI and locally injected ADSC-Exos to verify their efficacy.

RESULTS

ADSC-Exos can reduce reactive oxygen species (ROS) accumulation and cell damage induced by an excessive inflammatory response in HBMECs. ADSC-Exos inhibit ferroptosis induced by excessive inflammation and upregulate the expression of glutathione peroxidase 4(GPX4) in HBMECs. It can also effectively promote proliferation, migration, and vessel-like structure formation. In vitro, ADSC-Exos improved behavioral function after SCI and increased the number and density of blood vessels around the damaged spinal cord. Moreover, we found that ADSC-Exos could increase nuclear factor erythroid-2-related factor 2(NRF2) expression and nuclear translocation, thereby affecting the expression of solute carrier family 7 member 11(SLC7A11) and GPX4, and the NRF2 inhibitor ML385 could reverse the above changes.

CONCLUSION

Our results suggest that ADSC-Exos may inhibit ferroptosis and promote the recovery of vascular and neural functions after SCI through the NRF2/SLC7A11/GPX4 pathway. This may be a potential therapeutic mechanism for spinal cord injury.

Temporal profiling and validation of oxidative stress-related genes in spinal cord injury

Oxidative stress (OS) plays a pivotal role in the pathogenesis of spinal cord injury (SCI), yet its underlying mechanisms remain elusive. In this study, we explored the OS phenotype in a rat model of SCI. Subsequently, comprehensive bioinformatic analyses were conducted on microarray data pertaining to SCI (GSE45006). Notably, KEGG enrichment analysis revealed a pronounced enrichment of pivotal pathways, namely MAPK, FoxO, Apoptosis, NF-κB, TNF, HIF-1, and Chemokine across distinct phases of SCI. Furthermore, GO enrichment analysis highlighted the significance of biological processes including response to hypoxia, response to decrease oxygen levels, response to reactive oxygen species, cellular response to oxidative stress, reactive oxygen species metabolic process, and regulation of neuron death in the context of OS following SCI. Notably, our study underscores the prominence of nine genes, namely Itgb1, Itgam, Fn1, Icam1, Cd44, Cxcr4, Ptprc, Tlr4, and Tlr2 as OS key genes in SCI, consistently expressed in both the acute phase (1, 3, 7 days) and sub-acute phase (14 days). Subsequently, the relative mRNA expression of these key genes in different time points (1, 3, 7, 14 days) post-SCI. Finally, leveraging the DsigDB database, we predicted ten potential compounds potentially targeting OS and facilitating the repair of SCI, thus providing novel insights into the mechanisms underlying OS and identifying potential therapeutic targets for SCI.

Mesenchymal stem cell attenuates spinal cord injury by inhibiting mitochondrial quality control-associated neuronal ferroptosis

Ferroptosis is a newly discovered form of iron-dependent oxidative cell death and drives the loss of neurons in spinal cord injury (SCI). Mitochondrial damage is a critical contributor to neuronal death, while mitochondrial quality control (MQC) is an essential process for maintaining mitochondrial homeostasis to promote neuronal survival. However, the role of MQC in neuronal ferroptosis has not been clearly elucidated. Here, we further demonstrate that neurons primarily suffer from ferroptosis in SCI at the single-cell RNA sequencing level. Mechanistically, disordered MQC aggravates ferroptosis through excessive mitochondrial fission and mitophagy. Furthermore, mesenchymal stem cells (MSCs)-mediated mitochondrial transfer restores neuronal mitochondria pool and inhibits ferroptosis through mitochondrial fusion by intercellular tunneling nanotubes. Collectively, these results not only suggest that neuronal ferroptosis is regulated in an MQC-dependent manner, but also fulfill the molecular mechanism by which MSCs attenuate neuronal ferroptosis at the subcellular organelle level. More importantly, it provides a promising clinical translation strategy based on stem cell-mediated mitochondrial therapy for mitochondria-related central nervous system disorders.

Inhibition of Connexin43 Improves the Recovery of Spinal Cord Injury Against Ferroptosis via the SLC7A11/GPX4 Pathway

Ferroptosis plays a key role in the process of spinal cord injury (SCI). As a signal amplifier, connexin 43 (CX43) participates in cell death signal transduction and aggravates the propagation of injury. However, it remains unclear whether CX43 plays a regulatory role in ferroptosis after SCI. The SCI rat model was established by an Infinite Vertical Impactor to investigate the role of CX43 in SCI-induced ferroptosis. Ferrostatin-1 (Fer-1), an inhibitor of ferroptosis, and a CX43-specific inhibitor (Gap27) were administered by intraperitoneal injection. Behavioral analysis was assessed according to the Basso-Beattie-Bresnahan (BBB) Motor Rating Scale and the inclined plate test. The levels of ferroptosis-related proteins were estimated by qRT-PCR and western blotting, while the histopathology of neuronal injury induced by SCI was evaluated by immunofluorescence, Nissl, FJB and Perl's Blue staining. Meanwhile, transmission electron microscopy was used to observe the ultrastructural changes characteristic of ferroptosis. Gap27 strongly inhibited ferroptosis and therefore improved the functional recovery of SCI, which was similar to the treatment of Fer-1. Notably, the inhibition of CX43 decreased P-mTOR/mTOR expression and reversed the decrease in SLC7A11 induced by SCI. As a result, the levels of GPX4 and glutathione (GSH) increased, while the levels of the lipid peroxidation products 4-hydroxynonenal (4-HNE) and malondialdehyde (MDA) decreased. Together, inhibition of CX43 could alleviate ferroptosis after SCI. These findings reveal a potential mechanism of the neuroprotective role of CX43 after SCI and provide a new theoretical basis for clinical transformation and application.

USP7 regulates HMOX-1 via deubiquitination to suppress ferroptosis and ameliorate spinal cord injury in rats

Heme oxygenase 1 (HMOX-1) is overexpressed in spinal cord injury (SCI) and relevant to ferroptosis. Ubiquitin-specific-processing protease 7 (USP7) has unveiled its role in regulating HMOX-1 stabilization while its function in SCI remains unknown. This study is to explore the potential molecular mechanism of the USP7-HMOX-1 axis in ferroptosis in a SCI rat model. SCI was assessed with Basso, Beattie, Bresnahan locomotion evaluation, hematoxylin-eosin histological staining, and immunofluorescence detection of NeuN. Ferroptosis was assessed by detections of the iron content, malondialdehyde and glutathione levels, mitochondrial damage, and glutathione peroxidase 4, 4-hydroxynonenal, USP7, and HMOX-1 expression in spinal cord. Co-immunoprecipitation was used to detect the binding of USP7 to HMOX-1. The ubiquitination level of HMOX-1 was measured after USP7 overexpression. USP7 expression was downregulated and HMOX-1 expression was upregulated in SCI rat models. HMOX-1 or USP7 overexpression promoted motor function recovery, ameliorated spinal cord damage, increased NeuN expression, and blocked the occurrence of ferroptosis in SCI rat models. In SCI rats, USP7 directly bound to HMOX-1 and its overexpression promoted HMOX-1 expression via deubiquitination. To sum up, USP7 overexpression facilitated the expression of HMOX-1 through deubiquitination, thereby reducing ferroptosis and alleviating SCI.

Competing endogenous RNA network analysis of the molecular mechanisms of ischemic stroke

BACKGROUND

Ischemic stroke (IS) is a serious neurological disease that largely results in long-term disability and death. Extensive evidence has indicated that the activation of inflammation and ferroptosis significantly contribute to the development of IS pathology. However, the underlying molecular mechanism remains unclear. In this study, we aimed to identify potential biomarkers associated with IS through the construction of a competing endogenous RNA (ceRNA) network and to investigate the possible inflammatory and ferroptosis-related molecular mechanisms.

RESULTS

We identified 178 differentially expressed target messenger RNAs (DETmRNAs) associated with IS. As revealed through enrichment analysis, the DEmRNAs were mainly enriched in the inflammatory signaling pathways and also related to ferroptosis mechanism. The CIBERSORT algorithm showed immune infiltration landscapes in which the naïve B cells, naïve T cells, and monocytes had statistically different numbers in the cerebral infarction group compared with the control group. A ceRNA network was constructed in this study involving 44 long non-coding RNAs (lncRNAs), 15 microRNAs (miRNAs), and 160 messenger RNAs (mRNAs). We used the receiver operating characteristic (ROC) analysis to identify three miRNAs (miR-103a-3p, miR-140-3p, and miR-17-5p), one mRNA (TLR4), and one lncRNA (NEAT1) as the potential key biomarkers of the ceRNA network. The key mRNA and lncRNA were shown to be highly related to the ferroptosis mechanism of IS. The expression of these key biomarkers was also further validated by a method of quantitative real-time polymerase chain reaction in SH-SY5Y cells, and the validated results were consistent with the findings predicted by bioinformatics.

CONCLUSION

Our results suggest that the ceRNA network may exert an important role in the inflammatory and ferroptosis molecular mechanisms of IS, providing new insight into therapeutic IS targets.