Comprehensive analysis of aberrantly expressed long non‑coding RNAs, microRNAs, and mRNAs associated with the competitive endogenous RNA network in cervical cancer

Chen, Peng; Zhang, Weiyuan; Chen, Yu; Zheng, Xiaoli; Yang, Dong

doi:10.3892/mmr.2020.11120

Cited by 12 publications

(9 citation statements)

References 58 publications

(49 reference statements)

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“…A study from Rao et.al. found a correlation between low expression of EPB41L4A-AS1 and early-stage breast cancer [8], whereas two other studies reported an upregulation of EPB41L4A-AS1 in cervical and ovarian cancer [27, 28]. One of the studies identified EPB41L4A-AS1 as a central hub in a sub-network in cervical cancer.…”

Section: Discussionmentioning

confidence: 99%

“…One of the studies identified EPB41L4A-AS1 as a central hub in a sub-network in cervical cancer. Analysis indicated an interaction between EPB41L4A-AS1 and the genes CCND2 and VDAC1 via different microRNAs, proposing a potential role as a biomarker for disease progression and as a therapeutic target [27]. In the study from Zhou et.al, EPB41L4A-AS1 was categorized as a risky lncRNA linked to stage progression and poor clinical outcome in ovarian cancer, and might be a potential candidate for classification of patients into subgroups [28].…”

Section: Discussionmentioning

confidence: 99%

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The lncRNA EPB41L4A-AS1 regulates gene expression in the nucleus and exerts cell type-dependent effects on cell cycle progression

Samdal

Chawla

et al. 2021

Preprint

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The long non-coding RNA (lncRNA) EPB41L4A-AS1 is aberrantly expressed in various cancers and has been reported to be involved in metabolic reprogramming and as a repressor of the Warburg effect. Although the biological relevance of EPB41L4A-AS1 is evident, its functional role seems to vary depending on cell type and state of disease. By combining RNA sequencing and ChIP sequencing of cell cycle synchronized HaCaT cells we previously identified EPB41L4A-AS1 to be one of 59 lncRNAs with potential cell cycle functions. Here, we demonstrate that EPB41L4A-AS1 exists as bright foci and regulates gene expression in the nucleus in both cis and trans. Specifically, we find that EPB41L4A-AS1 positively regulates its sense overlapping gene EPB41L4A and influences expression of hundreds of other genes, including genes involved in cell proliferation. Finally, we show that EPB41L4A-AS1 affects cell cycle phase distribution, though these effects vary between cell types.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The lncRNA EPB41L4A-AS1 regulates gene expression in the nucleus and exerts cell type-dependent effects on cell cycle progression

Samdal

Chawla

et al. 2021

Preprint

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“…The ceRNA hypothesis [ 6 ] was first proposed in 2011, and posits that lncRNAs regulate the expression of target mRNAs by adsorbing miRNAs and thereby act as ceRNAs; they competitively bind to shared miRNAs, inhibiting the degradation of mRNA and thus acting as miRNA sponges. To date, the complex oncogenesis-related ceRNA network of lncRNA–miRNA–mRNA interactions has been explored in various types of cancer, such as colorectal cancer [ 7 ], cervical cancer [ 8 ], and lung squamous cell carcinoma [ 9 ]. However, ceRNA network analysis in patients with STAD is relatively rare.…”

Section: Introductionmentioning

confidence: 99%

Ferroptosis-related gene SLC1A5 is a novel prognostic biomarker and correlates with immune infiltrates in stomach adenocarcinoma

Zhu

et al. 2022

Cancer Cell Int

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Background Stomach adenocarcinoma (STAD) is associated with high morbidity and mortality rates. Ferroptosis is an iron-dependent form of cell death, which plays an important role in the development of many cancers. Tumor-associated competing endogenous RNAs (ceRNAs) regulate tumorigenesis and development. Our study aimed to construct ceRNA networks and explore the relationship between ferroptosis-related genes in the ceRNA network and immune infiltration in STAD. Methods Based on the interactions among long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs), a ceRNA network was constructed to illustrate the relationships among lncRNAs, miRNAs, and mRNAs. Subsequently, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) functional enrichment analyses were carried out to explore the functions and interactions of the differentially expressed (DE) mRNAs related to the ceRNA network. Differential expression and prognostic analysis of ferroptosis-related genes in the ceRNA network were performed using the R package “limma” and “survminer.” The correlation between ferroptosis-related genes and tumor-infiltrating immune cells was analyzed using Spearman correlation analysis and CIBERSORT. Quantitative real-time PCR (qRT-PCR) was used to validate the expression of ferroptosis-related genes in STAD cells lines. Results A ceRNA network consisting of 29 DElncRNAs, 31 DEmiRNAs, and 182 DEmRNAs was constructed. These DEmRNAs were significantly enriched in pathways related to the occurrence and development of STAD. The ferroptosis-related gene SLC1A5 was upregulated in STAD (P < 0.001) and was associated with better prognosis (P = 0.049). The CIBERSORT database and Spearman correlation analysis indicated that SLC1A5 was correlated with eight types of tumor-infiltrating immune cells and immune checkpoints, including PD-L1(CD-274) and PD-1(PDCD1). The SLC1A5 mRNA was found to be highly expressed in STAD cells lines. Conclusions Our study provides insights into the function of ceRNAs in STAD and identifies biomarkers for the development of therapies for STAD. The ferroptosis-related gene SLC1A5 in the ceRNA network was associated with both tumor-infiltrating immune cells and immune checkpoints in the tumor microenvironment, suggesting that SLC1A5 may be a novel prognostic marker and a potential target for STAD immunotherapy in the future.

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“…The famous competing endogenous RNA (ceRNA) hypothesis proposes that lncRNAs can act as ceRNAs to compete for miRNA response elements, thus regulating target mRNA expression ( Salmena et al, 2011 ). The function of such a ceRNA network has been verified in many cancers, including Wilms’ tumor ( Zheng et al, 2020 ) and cervical cancer ( Chen et al, 2020 ). However, the survival-related ceRNA network in GC needs further study.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Analysis of Survival-Related lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Gastric Cancer

Zhao

Zhang

et al. 2021

Front. Genet.

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To analyze and construct a survival-related endogenous RNA (ceRNA) network in gastric cancer (GC) with lymph node metastasis, we obtained expression profiles of long non-coding RNAs (lncRNAs), mRNAs, and microRNAs (miRNAs) in GC from The Cancer Genome Atlas database. The edgeR package was used to screen differentially expressed lncRNAs, mRNAs, and miRNAs between GC patients with lymphatic metastasis and those without lymphatic metastasis. Then, we used univariate Cox regression analysis to identify survival-related differentially expressed RNAs. In addition, we used multivariate Cox regression analysis to screen lncRNAs, miRNAs, and mRNAs for use in the prognostic prediction models. The results showed that 2,247 lncRNAs, 155 miRNAs, and 1,253 mRNAs were differentially expressed between the two patient groups. Using univariate Cox regression analysis, we found that 395 lncRNAs, eight miRNAs, and 180 mRNAs were significantly related to the survival time of GC patients. We next created a survival-related network consisting of 59 lncRNAs, seven miRNAs, and 36 mRNAs. In addition, we identified eight RNAs associated with prognosis by multivariate Cox regression analysis, comprising three lncRNAs (AC094104.2, AC010457.1, and AC091832.1), two miRNAs (miR-653-5p and miR-3923), and three mRNAs (C5orf46, EPHA8, and HPR); these were used to construct the prognostic prediction models, and their risk scores could be used to assess GC patients’ prognosis. In conclusion, this study provides new insights into ceRNA networks in GC and the screening of prognostic biomarkers for GC.

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Comprehensive analysis of aberrantly expressed long non‑coding RNAs, microRNAs, and mRNAs associated with the competitive endogenous RNA network in cervical cancer

Cited by 12 publications

References 58 publications

The lncRNA EPB41L4A-AS1 regulates gene expression in the nucleus and exerts cell type-dependent effects on cell cycle progression

The lncRNA EPB41L4A-AS1 regulates gene expression in the nucleus and exerts cell type-dependent effects on cell cycle progression

Ferroptosis-related gene SLC1A5 is a novel prognostic biomarker and correlates with immune infiltrates in stomach adenocarcinoma

Comprehensive Analysis of Survival-Related lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Gastric Cancer

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