Identification of Molecular Correlations Between DHRS4 and Progressive Neurodegeneration in Amyotrophic Lateral Sclerosis By Gene Co-Expression Network Analysis

Li, Shu; Zhu, Yu; Wei, Caihui; Li, Cheng; Chen, Wenzhi; Jiang, Shishi; Yuan, Dongxiang; Xu, Renshi

doi:10.3389/fimmu.2022.874978

Cited by 5 publications

(2 citation statements)

References 70 publications

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“…Cd74 deficiency could decrease peripheral lymphocyte activation and neurodegeneration following TBI, suggesting that targeting the switch between innate and adaptive immunity might be a potential therapeutic strategy [45]. C1qa, C1qb, and C1qc are three distinct subunits of complement component C1q, which is a crucial protein in the complement cascade within the innate immune system [71,72]. One recent clinical study showed that elevated serum C1q levels were significantly correlated with traumatic severity and could serve as an independent prognostic factor for long-term outcomes after TBI [73].…”

Section: Discussionmentioning

confidence: 99%

Identification of Key Genes and Pathways in the Hippocampus after Traumatic Brain Injury: Bioinformatics Analysis and Experimental Validation

Zeng¹,

Zhao²,

Zhao³

et al. 2023

J. Integr. Neurosci.

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Background: Traumatic brain injury (TBI) is a common brain injury with a high morbidity and mortality. The complex injury cascade triggered by TBI can result in permanent neurological dysfunction such as cognitive impairment. In order to provide new insights for elucidating the underlying molecular mechanisms of TBI, this study systematically analyzed the transcriptome data of the rat hippocampus in the subacute phase of TBI. Methods: Two datasets (GSE111452 and GSE173975) were downloaded from the Gene Expression Omnibus (GEO) database. Systematic bioinformatics analyses were performed, including differentially expressed genes (DEGs) analysis, gene set enrichment analysis (GSEA), Gene Ontology (GO) enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction (PPI) network construction, and hub gene identification. In addition, hematoxylin and eosin (HE), Nissl, and immunohistochemical staining were performed to assess the injured hippocampus in a TBI rat model. The hub genes identified by bioinformatics analyses were verified at the mRNA expression level. Results: A total of 56 DEGs were shared in the two datasets. GSEA results suggested significant enrichment in the MAPK and PI3K/Akt pathways, focal adhesion, and cellular senescence. GO and KEGG analyses showed that the common DEGs were predominantly related to immune and inflammatory processes, including antigen processing and presentation, leukocyte-mediated immunity, adaptive immune response, lymphocyte-mediated immunity, phagosome, lysosome, and complement and coagulation cascades. A PPI network of the common DEGs was constructed, and 15 hub genes were identified. In the shared DEGs, we identified two transcription co-factors and 15 immune-related genes. The results of GO analysis indicated that these immune-related DEGs were mainly enriched in biological processes associated with the activation of multiple cells such as microglia, astrocytes, and macrophages. HE and Nissl staining results demonstrated overt hippocampal neuronal damage. Immunohistochemical staining revealed a marked increase in the number of Iba1-positive cells in the injured hippocampus. The mRNA expression levels of the hub genes were consistent with the transcriptome data. Conclusions: This study highlighted the potential pathological processes in TBI-related hippocampal impairment. The crucial genes identified in this study may serve as novel biomarkers and therapeutic targets, accelerating the pace of developing effective treatments for TBI-related hippocampal impairment.

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Section: Discussionmentioning

confidence: 99%

Identification of Key Genes and Pathways in the Hippocampus after Traumatic Brain Injury: Bioinformatics Analysis and Experimental Validation

Zeng¹,

Zhao²,

Zhao³

et al. 2023

J. Integr. Neurosci.

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“…The fast development of bioinformatics provides a broad prospect for the research of disease diagnosis and therapeutic targets [26]. For example, Lee et al found that DLK2 acts as a potential prognostic biomarker for RCC based on bioinformatics analysis [27].…”

Section: Introductionmentioning

confidence: 99%

The Prognostic Value of lncRNA MCM3AP-AS1 on Clinical Outcomes in Various Cancers: A Meta- and Bioinformatics Analysis

Zhang

Wang

et al. 2022

Disease Markers

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Background. MCM3AP antisense RNA 1 (MCM3AP-AS1) is a newly identified potential tumor biomarker. Nevertheless, the prognostic value of MCM3AP-AS1 in cancer has been inconsistent in the available studies. We performed this meta-analysis to identify the prognostic role of MCM3AP-AS1 in various cancers. Methods. We searched PubMed, Web of Science, EMBASE, and the Cochrane Library databases to screen relevant studies. Hazard ratios (HR) or odds ratios (OR) and corresponding 95% confidence intervals (CI) were used to evaluate the relationship between aberrant MCM3AP-AS1 expression and survival and clinicopathological features (CFS) of cancer patients. A meta-analysis was performed using STATA 12.0 software. Additionally, results were validated by an online database based on The Cancer Genome Atlas (TCGA). Subsequently, we analyzed the MCM3AP-AS1-related genes and molecular mechanisms based on the MEM database. Results. Our results showed that overexpression of MCM3AP-AS1 was related to poor overall survival (OS) ( HR = 2.00 , 95% CI, 1.52–2.64, P < 0.001 ) and relapse-free survival (RFS) ( HR = 3.28 , 95% CI 1.56–6.88, P = 0.002 ). In addition, MCM3AP-AS1 overexpression was associated with TNM stage, differentiation grade, and lymph node metastasis, but not significantly with age, gender, and tumor size. In addition, MCM3AP-AS1 overexpression was verified by the GEPIA online database to be associated with poorer survival. The further functional investigation suggested that MCM3AP-AS1 may be involved in several cancer-related pathways. Conclusions. The overexpression of MCM3AP-AS1 was related to poor survival and CFS. MCM3AP-AS1 may be considered a novel prognostic marker and therapeutic target in various cancers.

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Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies

Reho,

Saez-Atienzar,

Ruffo

et al. 2024

Commun Biol

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Dementia with Lewy bodies (DLB) is a common form of dementia in the elderly population. We performed genome-wide DNA methylation mapping of cerebellar tissue from pathologically confirmed DLB cases and controls to study the epigenetic profile of this understudied disease. After quality control filtering, 728,197 CpG-sites in 278 cases and 172 controls were available for the analysis. We undertook an epigenome-wide association study, which found a differential methylation signature in DLB cases. Our analysis identified seven differentially methylated probes and three regions associated with DLB. The most significant CpGs were located in ARSB (cg16086807), LINC00173 (cg18800161), and MGRN1 (cg16250093). Functional enrichment evaluations found widespread epigenetic dysregulation in genes associated with neuron-to-neuron synapse, postsynaptic specialization, postsynaptic density, and CTCF-mediated synaptic plasticity. In conclusion, our study highlights the potential importance of epigenetic alterations in the pathogenesis of DLB and provides insights into the modified genes, regions and pathways that may guide therapeutic developments.

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Identification of Molecular Correlations Between DHRS4 and Progressive Neurodegeneration in Amyotrophic Lateral Sclerosis By Gene Co-Expression Network Analysis

Cited by 5 publications

References 70 publications

Identification of Key Genes and Pathways in the Hippocampus after Traumatic Brain Injury: Bioinformatics Analysis and Experimental Validation

Identification of Key Genes and Pathways in the Hippocampus after Traumatic Brain Injury: Bioinformatics Analysis and Experimental Validation

The Prognostic Value of lncRNA MCM3AP-AS1 on Clinical Outcomes in Various Cancers: A Meta- and Bioinformatics Analysis

Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies

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