Combination of machine learning-based bulk and single-cell genomics reveals necroptosis-related molecular subtypes and immunological features in autism spectrum disorder.

Background: Necroptosis is a novel form of controlled cell death that contributes to the progression of various illnesses. Nonetheless, the function and significance of necroptosis in autism spectrum disorders (ASD) remain unknown and require further investigation. Methods: We utilized single-nucleus RNA sequencing (snRNA-seq) data to assess the expression patterns of necroptosis in children with autism spectrum disorder (ASD) based on 159 necroptosis-related genes. We identified differentially expressed NRGs and used an unsupervised clustering approach to divide ASD children into distinct molecular subgroups. We also evaluated immunological infiltrations and immune checkpoints using the CIBERSORT algorithm. Characteristic NRGs, identified by the LASSO, RF, and SVM-RFE algorithms, were utilized to construct a risk model. Moreover, functional enrichment, immune infiltration, and CMap analysis were further explored. Additionally, external validation was performed using RT-PCR analysis. Results: Both snRNA-seq and bulk transcriptome data demonstrated a greater necroptosis score in ASD children. Among these cell subtypes, excitatory neurons, inhibitory neurons, and endothelials displayed the highest activity of necroptosis. Children with ASD were categorized into two subtypes of necroptosis, and subtype2 exhibited higher immune activity. Four characteristic NRGs (TICAM1, CASP1, CAPN1, and CHMP4A) identified using three machine learning algorithms could predict the onset of ASD. Nomograms, calibration curves, and decision curve analysis (DCA) based on 3-NRG have been shown to have clinical benefit in children with ASD. Furthermore, necroptosis-based riskScore was found to be positively associated with immune activation. Finally, RT-PCR demonstrated differentially expressed of these four NRGs in human peripheral blood samples. Conclusion: A comprehensive identification of necroptosis may shed light on the underlying pathogenic process driving ASD onset. The classification of necroptosis subtypes and construction of a necroptosis-related risk model may yield significant insights for the individualized treatment of children with ASD.

Identification of Ferroptosis-Related Molecular Clusters and Immune Characterization in Autism Spectrum Disorder.

Introduction: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with clinical presentation and prognostic heterogeneity. Ferroptosis is a regulated non-apoptotic cell death program implicated in the occurrence and progression of various diseases. Therefore, we aimed to explore ferroptosis-related molecular subtypes in ASD and further illustrate the potential mechanism. Methods: A total of 201 normal samples and 293 ASD samples were obtained from the Gene Expression Omnibus (GEO) database. We used the unsupervised clustering analysis to identify the molecular subtypes based on ferroptosis-related genes (FRGs) and evaluate the immune characteristics between ferroptosis subtypes. Ferroptosis signatures were identified using the least absolute shrinkage and selection operator regression (LASSO) and recursive feature elimination for support vector machines (SVM-RFE) machine learning algorithms. The ferroptosis scores based on seven selected genes were constructed to evaluate the ferroptosis characteristics of ASD. Results: We identified 16 differentially expressed FRGs in ASD children compared with controls. Two distinct molecular clusters associated with ferroptosis were identified in ASD. Analysis of immune infiltration revealed immune heterogeneity between the two clusters. Cluster2, characterized by a higher immune score and a larger number of infiltrated immune cells, exhibited a stronger immune response and was markedly enriched in immune response-related signaling pathways. Additionally, the ferroptosis scores model was capable of predicting ASD subtypes and immunity. Higher levels of ferroptosis scores were associated with immune activation, as seen in Cluster2. Lower ferroptosis scores were accompanied by relative immune downregulation, as seen in Cluster1. Conclusion: Our study systematically elucidated the intricate correlation between ferroptosis and ASD and provided a promising ferroptosis score model to predict the molecular clusters and immune infiltration cell profiles of children with ASD.

Downregulation of Three Immune-Specific Core Genes and the Regulatory Pathways in Children and Adult Friedreich's Ataxia: A Comprehensive Analysis Based on Microarray.

BACKGROUND: Friedreich's ataxia (FRDA) is a familial hereditary disorder that lacks available therapy. Therefore, the identification of novel biomarkers and key mechanisms related to FRDA progression is urgently required. METHODS: We identified the up-regulated and down-regulated differentially expressed genes (DEGs) in children and adult FRDA from the GSE11204 dataset and intersected them to determine the co-expressed DEGs (co-DEGs). Enrichment analysis was conducted and a protein-protein interaction (PPI) network was constructed to identify key pathways and hub genes. The potential diagnostic biomarkers were validated using the GSE30933 dataset. Cytoscape was applied to construct interaction and competitive endogenous RNA (ceRNA) networks. RESULTS: Gene Set Enrichment Analysis (GSEA) indicated that the genes in both the child and adult samples were primarily enriched in their immune-related functions. We identified 88 co-DEGs between child and adult FRDA samples. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome enrichment analysis suggested that these co-DEGs were primarily enriched in immune response, inflammatory reaction, and necroptosis. Immune infiltration analysis showed remarkable differences in the proportions of immune cell subtype between FRDA and healthy samples. In addition, ten core genes and one gene cluster module were screened out based on the PPI network. We verified eight immune-specific core genes using a validation dataset and found CD28, FAS, and ITIF5 have high diagnostic significance in FRDA. Finally, NEAT1-hsa-miR-24-3p-CD28 was identified as a key regulatory pathway of child and adult FRDA. CONCLUSIONS: Downregulation of three immune-specific hub genes, CD28, FAS, and IFIT5, may be associated with the progression of child and adult FRDA. Furthermore, NEAT1-hsa-miR-24-3p-CD28 may be the potential RNA regulatory pathway related to the pathogenesis of child and adult FRDA.

CXXC4 mediates glucose-induced ß-cell proliferation.

AIMS: CXXC finger protein 4 (CXXC4) is an identified negative regulator of the Wnt/ß-catenin pathway, and it is involved in cancer cell proliferation. In this study, we sought to clarify whether CXXC4 is involved in glucose-stimulated ß-cell proliferation. MATERIALS AND METHODS: We investigated the biological function of CXXC4 in glucose-induced ß-cell proliferation, and we investigated the underlying mechanism of this activity. First, we analyzed CXXC4 expression in established rat models treated for 24 h with a high glucose infusion and in INS-1 cells and primary rat islets treated with different concentrations of glucose. Subsequently, we used an adenovirus to overexpress CXXC4 in INS-1 cells and primary islets. The proliferation rate of ß-cells was evaluated by CCK-8 and EdU incorporation methods. Cell cycle analysis was performed by flow cytometry. Finally, the Wnt signaling pathway and its downstream genes were assessed by Western blot. RESULTS: CXXC4 mRNA levels were significantly lower in islets isolated from glucose-infused rats than they were in those isolated from saline-infused rats. Decreased expression of CXXC4 also correlated with high glucose treatment of INS-1 cells and primary rat ß-cells. Furthermore, adenovirus-mediated overexpression of CXXC4 inhibited cell proliferation induced by the high glucose treatment in vitro, which was mechanistically mediated by Wnt signaling and a decrease in cyclin D2 expression. CONCLUSIONS: Glucose inhibits CXXC4 expression and hence promotes pancreatic ß-cell proliferation. Our findings may provide a new potential target for the treatment of diabetes.

Severe hypoglycemia exacerbates myocardial dysfunction and metabolic remodeling in diabetic mice.

Although several studies have revealed that adverse cardiovascular events in diabetic patients are closely associated with severe hypoglycemia (SH), the causal relationship and related mechanisms remain unclear. This study aims to investigate whether SH promotes myocardial injury and further explores the potential mechanisms with focus on disturbances in lipid metabolism. SH promoted myocardial dysfunction and structural disorders in the diabetic mice but not in the controls. SH also enhanced the production of myocardial proinflammatory cytokines and oxidative stress. Moreover, myocardial lipid deposition developed in diabetic mice after SH, which was closely related to myocardial dysfunction and the inflammatory response. We further found that myocardial metabolic remodeling was associated with changes in PPAR-ß/δ and its target molecules in diabetic mice exposed to SH. These findings demonstrate that SH exacerbates myocardial dysfunction and the inflammatory response in diabetic mice, which may be induced by myocardial metabolic remodeling via PPAR-ß/δ.

Recurrent nonsevere hypoglycemia exacerbates imbalance of mitochondrial homeostasis leading to synapse injury and cognitive deficit in diabetes.

Recurrent nonsevere hypoglycemia (RH) can lead to cognitive dysfunction in patients with diabetes, although the involved mechanisms remain unclear. Here, we aimed to investigate the mechanism underlying RH-induced cognitive deficits with a focus on mitochondrial homeostasis. To establish a model that mimicked RH in patients with type 1 diabetes (T1DM) receiving insulin therapy, streptozotocin-induced mice with T1DM were subjected to recurrent, twice-weekly insulin injections over 4 wk. We found that RH disrupted the mitochondrial fine structure, reduced the number of mitochondria, and upregulated the expression of mitochondrial dynamics and mitophagy markers, including dynamin-related protein 1 (Drp1), Bcl-2/adenovirus E1B 19-kDa-interacting protein-3 (BNIP3), and microtubule-associated protein 1 light-chain 3 (LC3) in the hippocampus of T1DM mice. Moreover, RH and chronic hyperglycemia synergistically promoted the production of reactive oxygen species, impaired mitochondrial membrane potential, and suppressed mitochondrial energy metabolism. Under diabetic conditions, RH also altered the synaptic morphology and reduced the expression of synaptic marker proteins. Long-term recognition memory and spatial memory, assessed with the Morris water maze test, were also impaired. However, these effects were largely prevented by mitochondrial division inhibitor 1, a potent and selective Drp1 inhibitor. Thus, it appears that RH exacerbates the imbalance of mitochondrial homeostasis, leading to synapse injury and cognitive deficits in diabetes. The adjustment of mitochondrial homeostasis could serve as an effective neuroprotective approach when addressing low blood sugar conditions.