Integrated analysis of ceRNA network in hepatocellular carcinoma using bioinformatics analysis

Luo, Yu; Li, Hongjuan; Huang, Hongli; Xue, Ling; Li, Haiwen; Liu, Li; Fu, Haiyan

doi:10.1097/md.0000000000026194

Cited by 5 publications

(5 citation statements)

References 57 publications

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“…PKM is another rate-limiting enzyme in glycolysis. In mammals, four tissue-specific pyruvate kinases exist, including PKL, PKR, PKM1, and PKM2 ( 70 ). The PKM gene forms PKM1 and PKM2 through variable splicing.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive analysis of FOXM1 immune infiltrates, m6a, glycolysis and ceRNA network in human hepatocellular carcinoma

Xu,

Pei,

Cheng

et al. 2023

Front. Immunol.

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BackgroundForkhead box M1 (FOXM1) is a member of the Forkhead box (Fox) transcription factor family. It regulates cell mitosis, cell proliferation, and genome stability. However, the relationship between the expression of FOXM1 and the levels of m6a modification, immune infiltration, glycolysis, and ketone body metabolism in HCC has yet to be fully elucidated.MethodsTranscriptome and somatic mutation profiles of HCC were downloaded from the TCGA database. Somatic mutations were analyzed by maftools R package and visualized in oncoplots. GO, KEGG and GSEA function enrichment was performed on FOXM1 co-expression using R. We used Cox regression and machine learning algorithms (CIBERSORT, LASSO, random forest, and SVM-RFE) to study the prognostic value of FOXM1 and immune infiltrating characteristic immune cells in HCC. The relationship between FOXM1 and m6A modification, glycolysis, and ketone body metabolism were analyzed by RNA-seq and CHIP-seq. The competing endogenous RNA (ceRNA) network construction relies on the multiMiR R package, ENCORI, and miRNET platforms.ResultsFOXM1 is highly expressed in HCC and is associated with a poorer prognosis. At the same time, the expression level of FOXM1 is significantly related to the T, N, and stage. Subsequently, based on the machine learning strategies, we found that the infiltration level of T follicular helper cells (Tfh) was a risk factor affecting the prognosis of HCC patients. The high infiltration of Tfh was significantly related to the poor overall survival rate of HCC. Besides, the CHIP-seq demonstrated that FOXM1 regulates m6a modification by binding to the promoter of IGF2BP3 and affects the glycolytic process by initiating the transcription of HK2 and PKM in HCC. A ceRNA network was successfully obtained, including FOXM1 - has-miR-125-5p – DANCR/MIR4435-2HG ceRNA network related to the prognosis of HCC.ConclusionOur study implicates that the aberrant infiltration of Tfh associated with FOXM1 is a crucial prognostic factor for HCC patients. FOXM1 regulates genes related to m6a modification and glycolysis at the transcriptional level. Furthermore, the specific ceRNA network can be used as a potential therapeutic target for HCC.

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Section: Discussionmentioning

confidence: 99%

Comprehensive analysis of FOXM1 immune infiltrates, m6a, glycolysis and ceRNA network in human hepatocellular carcinoma

Xu,

Pei,

Cheng

et al. 2023

Front. Immunol.

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“…Notably, a large number of previous studies have explored the lncRNA/miRNA/mRNA ceRNA network in HCC [ 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 ]. In contrast to these studies, the present study is the first to investigate the lncRNA/miRNA/mRNA ceRNA network in HCV-related HCC, and the network was associated with patient prognosis.…”

Section: Discussionmentioning

confidence: 99%

Construction of novel lncRNA-miRNA-mRNA ceRNA networks associated with prognosis of hepatitis C virus related hepatocellular carcinoma

Shao

Liu

Fang

et al. 2022

Heliyon

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“…IncRNAs can exert miRNA sponge effects through the ceRNA mechanism [ 38 ]. In this study, we found that miR-129-5p was negatively regulated by PCGEM1 and negatively correlated with PCGEM1 in PCa.…”

Section: Discussionmentioning

confidence: 99%

Long non-coding RNA-PCGEM1 contributes to prostate cancer progression by sponging microRNA miR-129-5p to enhance chromatin licensing and DNA replication factor 1 expression

Wang

Yang

et al. 2022

Bioengineered

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PCGEM1 facilitates prostate cancer (PCa) progression. This study aimed to elucidate the mechanism of action of PCGEM1 in PCa. The expression of PCGEM1, microRNA miR-129-5p, chromatin licensing, and DNA replication factor 1 (CDT1) was detected by quantitative reverse transcription-PCR (qRT-PCR). A series of function experiments including cell counting kit-8 (CCK-8), caspase-3 activity, and cell cycle assays were performed to evaluate the influence of PCGEM1, miR-129-5p, and CDT1 on the biological processes of PCa cells. CyclinD1, cyclin dependent kinase 4 (CDK4), Bax, and Bcl-2 protein levels were measured by western blotting. Subcellular isolation revealed the distribution of PCa cells. The connections between PCGEM1, miR-129-5p, and CDT1 were evaluated by luciferase, RIP assay, and Pearson correlation analysis. Both PCGEM1 and CDT1 were upregulated in PCa, while miR-129-5p was downregulated and negatively correlated with PCGEM1 and CDT1. Downregulation of PCGEM1 or CDT1 inhibited the viability, promoted apoptosis and cycle arrest of PCa cells in vitro , and controlled tumor growth in vivo . PCGEM1 plays a crucial role in the progression of PCa by sponging miR-129-5p as a ceRNA of CDT1. PCGEM1 is a CDT1-dependent PCa promoter site that absorbs miR-129-5p.

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Integrated analysis of ceRNA network in hepatocellular carcinoma using bioinformatics analysis

Cited by 5 publications

References 57 publications

Comprehensive analysis of FOXM1 immune infiltrates, m6a, glycolysis and ceRNA network in human hepatocellular carcinoma

Comprehensive analysis of FOXM1 immune infiltrates, m6a, glycolysis and ceRNA network in human hepatocellular carcinoma

Construction of novel lncRNA-miRNA-mRNA ceRNA networks associated with prognosis of hepatitis C virus related hepatocellular carcinoma

Long non-coding RNA-PCGEM1 contributes to prostate cancer progression by sponging microRNA miR-129-5p to enhance chromatin licensing and DNA replication factor 1 expression

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