Integrated Bioinformatic Analysis of DNA Methylation and Immune Infiltration in Endometrial Cancer

Dai, Fangfang; Wu, Jinglin; Deng, Zhanfeng; Li, Hengxing; Tan, Wei; Yuan, Mengqin; Yang, Dongyong; Liu, Shiyi; Zheng, Y.; Hu, Min; Yuan, Chaoyan; Cheng, Yanxiang

doi:10.1155/2022/5119411

Cited by 11 publications

(4 citation statements)

References 40 publications

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“…Bubble plots and circular plots were generated to visualize the enrichment results of the three categories, namely Biological Processes (BP), Cellular Components (CC), and Molecular Functions (MF), in the Gene Ontology (GO). Additionally, a bubble plot was generated to display the enrichment results of the KEGG pathway analysis [ 46 ].…”

Section: Methodsmentioning

confidence: 99%

NOX4-mediated astrocyte ferroptosis in Alzheimer’s disease

Maimaiti,

Su,

Zhang

et al. 2024

Cell Biosci

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This study investigates NADPH oxidase 4 (NOX4) involvement in iron-mediated astrocyte cell death in Alzheimer’s Disease (AD) using single-cell sequencing data and transcriptomes. We analyzed AD single-cell RNA sequencing data, identified astrocyte marker genes, and explored biological processes in astrocytes. We integrated AD-related chip data with ferroptosis-related genes, highlighting NOX4. We validated NOX4’s role in ferroptosis and AD in vitro and in vivo. Astrocyte marker genes were enriched in AD, emphasizing their role. NOX4 emerged as a crucial player in astrocytic ferroptosis in AD. Silencing NOX4 mitigated ferroptosis, improved cognition, reduced Aβ and p-Tau levels, and alleviated mitochondrial abnormalities. NOX4 promotes astrocytic ferroptosis, underscoring its significance in AD progression.

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Section: Methodsmentioning

confidence: 99%

NOX4-mediated astrocyte ferroptosis in Alzheimer’s disease

Maimaiti,

Su,

Zhang

et al. 2024

Cell Biosci

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“…Bubble plots were generated to visualize the enrichment results for three Gene Ontology (GO) categories: biological process (BP), cellular component (CC), and molecular function (MF). Furthermore, a separate bubble plot was created for the KEGG enrichment analysis results [ 23 ].…”

Section: Methodsmentioning

confidence: 99%

Targeting CSF1R in myeloid-derived suppressor cells: insights into its immunomodulatory functions in colorectal cancer and therapeutic implications

Tong,

Qiao,

Dong

et al. 2024

J Nanobiotechnol

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Objective This study aimed to investigate the critical role of MDSCs in CRC immune suppression, focusing on the CSF1R and JAK/STAT3 signaling axis. Additionally, it assessed the therapeutic efficacy of LNCs@CSF1R siRNA and anti-PD-1 in combination. Methods Single-cell transcriptome sequencing data from CRC and adjacent normal tissues identified MDSC-related differentially expressed genes. RNA-seq analysis comprehensively profiled MDSC gene expression in murine CRC tumors. LNCs@CSF1R siRNA nanocarriers effectively targeted and inhibited CSF1R. Flow cytometry quantified changes in MDSC surface markers post-CSF1R inhibition. RNA-seq and pathway enrichment analyses revealed the impact of CSF1R on MDSC metabolism and signaling. The effect of CSF1R inhibition on the JAK/STAT3 signaling axis was validated using Colivelin and metabolic assessments. Glucose and fatty acid uptake were measured via fluorescence-based flow cytometry. The efficacy of LNCs@CSF1R siRNA and anti-PD-1, alone and in combination, was evaluated in a murine CRC model with extensive tumor section analyses. Results CSF1R played a significant role in MDSC-mediated immune suppression. LNCs@CSF1R siRNA nanocarriers effectively targeted MDSCs and inhibited CSF1R. CSF1R regulated MDSC fatty acid metabolism and immune suppression through the JAK/STAT3 signaling axis. Inhibition of CSF1R reduced STAT3 activation and target gene expression, which was rescued by Colivelin. Combined treatment with LNCs@CSF1R siRNA and anti-PD-1 significantly slowed tumor growth and reduced MDSC abundance within CRC tumors. Conclusion CSF1R via the JAK/STAT3 axis critically regulates MDSCs, particularly in fatty acid metabolism and immune suppression. Combined therapy with LNCs@CSF1R siRNA and anti-PD-1 enhances therapeutic efficacy in a murine CRC model, providing a strong foundation for future clinical applications.

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“…The corrplot of “R” ( 27 ) was used to create the heat maps related to invasive immune cells, and Cibersort ( 28 ) was utilized to examine the infiltration of immune cells.…”

Section: Methodsmentioning

confidence: 99%

Schizophrenia and cell senescence candidate genes screening, machine learning, diagnostic models, and drug prediction

Feng

Shen

et al. 2023

Front. Psychiatry

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BackgroundSchizophrenia (SC) is one of the most common psychiatric diseases. Its potential pathogenic genes and effective treatment methods are still unclear. Cell senescence has been confirmed in mental diseases. A link exists between cellular senescence and immunity, and immune-related problems affect suicide rates in individuals suffering from schizophrenia. Therefore, the aims of this study were to identify candidate genes based on cell senescence that can affect the diagnosis and treatment of schizophrenia.MethodsTwo data sets of schizophrenia were provided by the Gene Expression Omnibus (GEO) database, one was taken as training and the other as a validation group. The genes related to cell senescence were obtained from the CellAge database. DEGs were identified using the Limma package and weighted gene co-expression network analysis (WGCNA). The function enrichment analysis was conducted, followed by machine learning-based identification for least absolute shrinking and selection operators (LASSO) regression. Random Forest were used to identify candidate immune-related central genes and establish artificial neural networks for verification of the candidate genes. The receiver operating characteristic curve (ROC curve) was used for the diagnosis of schizophrenia. Immune cell infiltrates were constructed to study immune cell dysregulation in schizophrenia, and relevant drugs with candidate genes were collected from the DrugBank database.ResultsThirteen co-expression modules were screened for schizophrenia, of which 124 were the most relevant genes.There were 23 intersected genes of schizophrenia (including DEGs and the cellular senescence-related genes), and through machine learning six candidate genes were finally screened out. The diagnostic value was evaluated using the ROC curve data. Based on these results it was confirmed that these candidate genes have high diagnostic value.Two drugs related to candidate genes, Fostamatinib and Ritodine, were collected from the DrugBanks database.ConclusionSix potential candidate genes (SFN, KDM5B, MYLK, IRF3, IRF7, and ID1) had been identified, all of which had diagnostic significance. Fostamatinib might be a drug choice for patients with schizophrenia to develop immune thrombocytopenic purpura (ITP) after treatment, providing effective evidence for the pathogenesis and drug treatment of schizophrenia.

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Integrated Bioinformatic Analysis of DNA Methylation and Immune Infiltration in Endometrial Cancer

Cited by 11 publications

References 40 publications

NOX4-mediated astrocyte ferroptosis in Alzheimer’s disease

NOX4-mediated astrocyte ferroptosis in Alzheimer’s disease

Targeting CSF1R in myeloid-derived suppressor cells: insights into its immunomodulatory functions in colorectal cancer and therapeutic implications

Schizophrenia and cell senescence candidate genes screening, machine learning, diagnostic models, and drug prediction

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