Identification of hepatocellular carcinoma-related genes associated with macrophage differentiation based on bioinformatics analyses

Cao, Jun; Zhang, Chi; Jiang, Guo‐Qing; Jin, Sheng‐Jie; Wang, Qian; Wang, Aoqing; Bai, Dou‐Sheng

doi:10.1080/21655979.2020.1868119

Cited by 16 publications

(15 citation statements)

References 48 publications

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“…Although CDC42SE2 could not be validated in the current study, a previous study confirmed the importance of CDC42 in bone metabolism and bone deterioration [ 33 , 34 ]. In addition, CDC42 is closely correlated with immunity and inflammation [ 35 ]. Osteoclastogenesis and bone resorption can be suppressed by inhibiting CDC42 activity [ 36 ].…”

Section: Discussionmentioning

confidence: 99%

Low expression of TCP1 (T-Complex 1) and PSMC1 (Proteasome 26S subunit, ATPase 1) in heterotopic ossification during ankylosing spondylitis

et al. 2021

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Heterotopic ossification (HO) is frequently seen in patients with spinal injuries. Therefore, this study aimed to characterize the association of HO with ankylosing spondylitis (AS) through gene expression profiling. The human transcriptomic datasets (GSE73754 and GSE94683) were obtained from the Gene Expression Omnibus database for analysis. Overlapping differentially expressed genes (DEGs) were identified between AS and HO disease states. Subsequently, weighted gene co-expression network analysis (WGCNA) was performed for constructing and identifying hub genes for each condition. Finally, a consensus of the overlapping DEGs and the hub genes in AS and HO was taken for determining the key genes involved in AS-induced HO. Quantitative realtime polymerase chain reaction and western blotting were used to detect the mRNA and protein expression levels in mesenchymal stem cells of AS patients and controls. Additionally, immunohistochemistry was performed on interspinous ligament samples for experimental validation of genes. DEG analysis identified 355 overlapping genes between HO and AS. WGCNA indicated that the salmon module of the 22 modules constructed, was most significantly correlated with ASinduced HO. Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of the salmon module indicated the presence of genes enriched in proteasome regulatory particle and proteasome pathways. mRNA expression analysis identified TCP1 and PSMC1 as the key genes in AS-induced HO. Further validation of these genes could help elucidate their role in the complex association of AS and HO.

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Section: Discussionmentioning

confidence: 99%

Low expression of TCP1 (T-Complex 1) and PSMC1 (Proteasome 26S subunit, ATPase 1) in heterotopic ossification during ankylosing spondylitis

et al. 2021

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“…Wnt/β-catenin signaling pathway is the ‘star pathway’ in cancer research [ 12 , 13 ]. In GC, the activation of Wnt/β-catenin signaling regulates the biological behaviors of cancer cells.…”

Section: Introductionmentioning

confidence: 99%

Male-specific long non-coding RNA testis-specific transcript, Y-linked 15 promotes gastric cancer cell growth by regulating Wnt family member 1/β-catenin signaling by sponging microRNA let-7a-5p

Zheng

Peng

Wu³

et al. 2022

Bioengineered

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The present study is aimed to investigate the regulatory effects and related mechanism of long non-coding RNA testis-specific transcript, Y-linked 15 (TTTY15) in gastric carcinoma (GC) cell proliferation, migration, invasion, apoptosis and epithelial–mesenchymal transition (EMT). TTTY15 expression in GC tissue samples and cells was detected by quantitative real-time PCR (qRT-PCR), and the correlation between TTTY15 expression and GC clinicopathological indicators was analyzed. Cell counting kit-8 (CCK-8), BrdU, flow cytometry and Transwell assays were performed for detecting GC cell proliferation, migration, invasion and apoptosis. Western blot was performed for detecting the expressions of EMT-associated proteins (N-cadherin and E-cadherin), Wnt family member 1 (Wnt1) protein and β-catenin protein. Bioinformatics analysis was conducted to predict, and RNA immunoprecipitation (RIP) assay and dual-luciferase reporter gene assay were performed to verify the targeted relationships of microRNA let-7a-5p (let-7a-5p) with TTTY15 and Wnt1 mRNA 3'UTR. It was found that TTTY15 expression was significantly up-regulated in GC tissues and cells, and was associated with advanced TNM stage and poor tumor differentiation. TTTY15 overexpression promoted GC cell proliferation, migration and invasion, the expressions of N-cadherin, Wnt1 and β-catenin protein, and inhibited the apoptosis and E-cadherin expression, while knocking down TTTY15 had the opposite effects. TTTY15 directly targeted let-7a-5p and negatively regulated its expression. Wnt1 was the target gene of let-7a-5p, and TTTY15 could indirectly and positively regulate Wnt1 expression. In conclusion, TTTY15 promotes GC progression, by regulating the let-7a-5p/Wnt1 axis to activate the Wnt/β-catenin pathway.

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“…These above results may be interfered by possible confounding factors, which were insufficient to reflect the direct effect of aging on skeletal muscle. Bioinformatics is a powerful tool for identifying hub genes in various diseases [12][13][14], therefore it was necessary to give a comprehensive analysis of the mechanism and biomarkers related to skeletal muscle aging, as well as the use of the linear analysis method.…”

Section: Introductionmentioning

confidence: 99%

Declined expressions of vast mitochondria-related genes represented by CYCS and transcription factor ESRRA in skeletal muscle aging

Kan

et al. 2021

Bioengineered

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Age-related skeletal muscle deterioration (sarcopenia) has a significant effect on the elderly's health and quality of life, but the molecular and gene regulatory mechanisms remain largely unknown. It is necessary to identify the candidate genes related to skeletal muscle aging and prospective therapeutic targets for effective treatments. The age-line-related genes (ALRGs) and age-line-related transcripts (ALRTs) were investigated using the gene expression profiles of GSE47881 and GSE118825 from the Gene Expression Omnibus (GEO) database. The proteinprotein interaction (PPI) networks were performed to identify the key molecules with Cytoscape, and Gene Set Enrichment Analysis (GSEA) was used to clarify the potential molecular functions. Two hub molecules were finally obtained and verified with quantitative real-time PCR (qRT-PCR). The results showed that the expression of mitochondria genes involved in mitochondrial electron transport, complex assembly of the respiratory chain, tricarboxylic acid cycle, oxidative phosphorylation, and ATP synthesis were down-regulated in skeletal muscle with aging. We further identified a primary hub gene of CYCS (Cytochrome C) and a key transcription factor of ESRRA (Estrogen-related Receptor Alpha) to be associated closely with skeletal muscle aging. PCR analysis confirmed the expressions of CYCS and ESRRA in gastrocnemius muscles of mice of different ages were significantly different, and decreased gradually with age. In conclusion, the main cause of skeletal muscle aging may be the systematically reduced expression of mitochondrial functional genes. The CYCS and ESRRA may play significant roles in the progression of skeletal muscle aging and serve as potential biomarkers for future diagnosis and treatment.

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Identification of hepatocellular carcinoma-related genes associated with macrophage differentiation based on bioinformatics analyses

Cited by 16 publications

References 48 publications

Low expression of TCP1 (T-Complex 1) and PSMC1 (Proteasome 26S subunit, ATPase 1) in heterotopic ossification during ankylosing spondylitis

Low expression of TCP1 (T-Complex 1) and PSMC1 (Proteasome 26S subunit, ATPase 1) in heterotopic ossification during ankylosing spondylitis

Male-specific long non-coding RNA testis-specific transcript, Y-linked 15 promotes gastric cancer cell growth by regulating Wnt family member 1/β-catenin signaling by sponging microRNA let-7a-5p

Declined expressions of vast mitochondria-related genes represented by CYCS and transcription factor ESRRA in skeletal muscle aging

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