&lt;p&gt;Transcriptome-Wide 5-Methylcytosine Functional Profiling of Long Non-Coding RNA in Hepatocellular Carcinoma&lt;/p&gt;

He, Yuting; Shi, Qingmiao; Zhang, Yize; Yuan, Xin; Yu, Zujiang

doi:10.2147/cmar.s262450

Cited by 22 publications

(19 citation statements)

References 44 publications

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“…Studies have also shown that m 5 Crelated regulators play essential roles in tumor progression in HCC (11,12). Research into m 5 C modifications has also provided evidence for the epigenetic m 5 C regulation of lncRNA related to HCC tumorigenesis and progression (13). However, the specific genomic distribution of m 5 C-related genes for HCC remains unclear.…”

Section: Introductionmentioning

confidence: 99%

Multi-Omic Analyses of the m5C Regulator ALYREF Reveal Its Essential Roles in Hepatocellular Carcinoma

Xue

Zhao

et al. 2021

Front. Oncol.

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The ALYREF protein acts as a crucial epigenetic regulator in several cancers. However, the specific expression levels and functional roles of ALYREF in cancers are largely unknown, including for hepatocellular carcinoma (HCC). In a pan-cancer tissue analysis that included HCC, we assessed the expression of ALYREF compared to normal tissues using The Cancer Genome Atlas database. Associations between ALYREF gene expression and the clinical characteristics of HCC patient samples were assessed using the UALCAN database. Kaplan-Meier plots were performed to assess HCC patient prognosis, and the TIMER database was used to explore associations between ALYREF expression and immune-cell infiltrations. The same methods were used to assess eIF4A3 expression in HCC patient samples. In addition, ALYREF- and elF4A3-related differentially expressed genes (DEGs) were determined using LinkedOmics, associated protein functionalities were predicted for positively associated DEGs, and both the TargetScan and miRDB databases were used to predict potential upstream miRNAs for control of ALYREF and eIF4A3 expression. We found that ALYREF gene expression was dysregulated in several cancers and was significantly elevated in HCC patient tissue samples and HCC cell lines. The overexpression of ALYREF was significantly related to both advanced tumor-node-metastasis stages and poor HCC prognosis. Furthermore, we found that eIF4A3 expression was significantly correlated with ALYREF expression, and that upregulated eIF4A3 was significantly associated with poor HCC patient outcomes. In the protein-protein interaction network, we identified eight hub genes based on the positively associated DEGs in common between ALYREF and eIF4A3, and the high expression levels of these hub genes were positively associated with patient clinical outcomes. In addition, we identified miR-4666a-5p and miR-6124 as potential regulators of ALYREF and eIF4A3 expression. These findings suggest that increased ALYREF expression may function as a novel biomarker for both HCC diagnosis and prognosis predictions.

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Section: Introductionmentioning

confidence: 99%

Multi-Omic Analyses of the m5C Regulator ALYREF Reveal Its Essential Roles in Hepatocellular Carcinoma

Xue

Zhao

et al. 2021

Front. Oncol.

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“…Studies have performed quantitative mapping of the m5C sites in Arabidopsis thaliana on a transcriptome range, and found more than 1000 m5C sites in mRNA, long non-coding RNA and other non-coding RNAs ( David et al, 2017 ). He et al (2020a) found that compared with adjacent non-tumor tissues, lncRNA m5C methylation occurs more frequently in Hepatocellular Carcinoma(HCC), and more methylated genes are up-regulated. KEGG pathway enrichment analysis show that hypermethylated genes are closely related to cancer pathways.…”

Section: Discussionmentioning

confidence: 99%

m5C-Related lncRNAs Predict Overall Survival of Patients and Regulate the Tumor Immune Microenvironment in Lung Adenocarcinoma

Pan

Huang

2021

Front. Cell Dev. Biol.

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Long non-coding RNAs (lncRNAs), which are involved in the regulation of RNA methylation, can be used to evaluate tumor prognosis. lncRNAs are closely related to the prognosis of patients with lung adenocarcinoma (LUAD); thus, it is crucial to identify RNA methylation-associated lncRNAs with definitive prognostic value. We used Pearson correlation analysis to construct a 5-Methylcytosine (m5C)-related lncRNAs–mRNAs coexpression network. Univariate and multivariate Cox proportional risk analyses were then used to determine a risk model for m5C-associated lncRNAs with prognostic value. The risk model was verified using Kaplan–Meier analysis, univariate and multivariate Cox regression analysis, and receiver operating characteristic curve analysis. We used principal component analysis and gene set enrichment analysis functional annotation to analyze the risk model. We also verified the expression level of m5C-related lncRNAs in vitro. The association between the risk model and tumor-infiltrating immune cells was assessed using the CIBERSORT tool and the TIMER database. Based on these analyses, a total of 14 m5C-related lncRNAs with prognostic value were selected to build the risk model. Patients were divided into high- and low-risk groups according to the median risk score. The prognosis of the high-risk group was worse than that of the low-risk group, suggesting the good sensitivity and specificity of the constructed risk model. In addition, 5 types of immune cells were significantly different in the high-and low-risk groups, and 6 types of immune cells were negatively correlated with the risk score. These results suggested that the risk model based on 14 m5C-related lncRNAs with prognostic value might be a promising prognostic tool for LUAD and might facilitate the management of patients with LUAD.

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“…Second, the modification of lncRNAs could mediate transcription repression [ 54 ]. Third, lncRNA modifications might alter its subcellular distribution [ 185 , 186 ]. Finally, lncRNA modifications regulate the stability of lncRNAs like H19, MALAT1, XIST, etc.…”

Section: Discussionmentioning

confidence: 99%

Long Non-Coding RNA Epigenetics

Kazimierczyk

Wrzesiński

2021

IJMS

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Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to understanding these processes. The characteristics of the individual methylases, pseudouridine synthases and adenine–inosine editing enzymes and the methods of lncRNA epigenetics for the detection of modified nucleosides, as well as the advantages and disadvantages of these methods, are discussed in detail. The final sections are devoted to the role of modifications in the most abundant lncRNAs and their functions in pathogenic processes.

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<p>Transcriptome-Wide 5-Methylcytosine Functional Profiling of Long Non-Coding RNA in Hepatocellular Carcinoma</p>

Cited by 22 publications

References 44 publications

Multi-Omic Analyses of the m5C Regulator ALYREF Reveal Its Essential Roles in Hepatocellular Carcinoma

Multi-Omic Analyses of the m5C Regulator ALYREF Reveal Its Essential Roles in Hepatocellular Carcinoma

m5C-Related lncRNAs Predict Overall Survival of Patients and Regulate the Tumor Immune Microenvironment in Lung Adenocarcinoma

Long Non-Coding RNA Epigenetics

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