Comprehensive biological function analysis of lncRNAs in hepatocellular carcinoma

Wang, Dan Dan; Chen, Fengjiao; Zeng, Tao; Tang, Qingxia; Chen, Bing; Chen, Ling; Yan, Dong; Li, Xiaosong

doi:10.1016/j.gendis.2019.12.013

Cited by 10 publications

(7 citation statements)

References 120 publications

(123 reference statements)

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“…ADIPOQ, which was identified as an adipose gene in 1996 [64] , might be a candidate gene for renal disease and diabetes [65] . AL356479.1 has – as MALAT1 – been associated with breast cancer [66] and appears to have significant effect on breast cancer survival [67] . This could be due to the majority of the tissue donors in Emont et al’s study being female [18] and might indicate existing or future health problems for some of the study participants, or might indicate a so far unknown function of AL356479.1 in adipocytes.…”

Section: Discussionmentioning

confidence: 99%

Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning

Caliskan

Çalışkan

Rasbach

et al. 2023

Computational and Structural Biotechnology Journal

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Section: Discussionmentioning

confidence: 99%

Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning

Caliskan

Çalışkan

Rasbach

et al. 2023

Computational and Structural Biotechnology Journal

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“…Numerous previous studies have demonstrated that lncRNAs play regulatory roles in various biological processes, including the cell cycle, cell differentiation, apoptosis, migration, invasion, and cancer progression (13)(14)(15)(16)(17). There is accumulating evidence that lncRNAs may also act as competing endogenous RNAs (ceRNAs) that are able to adsorb microRNAs (miRNAs/ miRs), and thus influence tumorigenesis (18,19). For example, lncRNA long intergenic non-protein coding RNA 2620 (BCRT1) was found to promote breast cancer progression by binding with miR-1303 (20).…”

Section: Introductionmentioning

confidence: 99%

The lncRNA TERC promotes gastric cancer cell proliferation, migration, and invasion by sponging miR-423-5p to regulate SOX12 expression

Wang¹,

Wu²,

Chang³

et al. 2022

Ann Transl Med

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Background: Long non-coding RNAs (lncRNAs) play critical roles in gastric cancer (GC) initiation progression. However, the biological function of the lncRNA telomerase RNA component (TERC) remains unknown in human GC. The present study sought to determine the biological function and underlying molecular mechanism of the lncRNA TERC in GC progression. Methods:The expression levels of the lncRNA TERC in GC tissues and cell lines were analyzed using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The effects of the lncRNA TERC on the proliferation, migration, and invasion of GC cells were determined using Cell Counting Kit-8 (CCK-8) and Transwell assays. Dual luciferase reporter and argonaute 2 (AGO2)-RNA immunoprecipitation (RIP) assays were used to detect the binding between the lncRNA TERC and microRNA-423-5p (miR-423-5p).Western blotting was performed to measure the expression levels of sex determining region Y-box 12 (SOX12), N-cadherin, E-cadherin, matrix metallopeptidase 9 (MMP9), and proliferating cell nuclear antigen (PCNA). Results:The results demonstrated that the lncRNA TERC expression levels were upregulated in GC cells and tissues, while miR-423-5p expression levels were downregulated. The upregulation of the lncRNA TERC was associated with a shorter overall survival in patients with GC. The knockdown of the lncRNA TERC significantly reduced the proliferation, migration, and invasion of human GC cell lines HGC-27 and SNU-1 cells. Further, the lncRNA TERC knockdown in the HGC-27 and SNU-1 cells significantly downregulated the expression levels of SOX12, N-cadherin, MMP9, and PCNA, and upregulated the expression levels of miR-423-5p and E-cadherin. MiR-423-5p was also identified as a target of the lncRNA TERC and was found to directly bind to the lncRNA TERC. Additionally, miR-423-5p was found to directly target SOX12 to inhibit the proliferation, migration, and invasion of the HGC-27 and SNU-1 cells. Conclusions:In conclusion, the findings of this study suggested that the lncRNA TERC may regulate the miR-423-5p/SOX12 signaling axis by directly sponging miR-423-5p and inhibiting SOX12 expression, thereby leading to the progression of GC. These findings may reveal novel targets for future GC therapy.

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“…Tumor hypoxia is one of the adverse factors for cancer treatment, and it participates in HCC occurrence and significantly increases HCC invasiveness [ 7 ]. LncRNA can act on miRNA to further target and regulate mRNA, all of which form the lncRNA/miRNA/mRNA regulatory axis, and then participate in the occurrence, development and metastasis of hepatocellular carcinoma [ 16 , 17 ]. The construction of the ceRNA networks under hypoxia is helpful for us to comprehend the molecular mechanism of hypoxia-related genes in hepatocellular carcinoma and find new prognostic markers and treatment entry points for hepatocellular carcinoma.…”

Section: Discussionmentioning

confidence: 99%

Identification of Hypoxia-Related Prognostic Signature and Competing Endogenous RNA Regulatory Axes in Hepatocellular Carcinoma

Tang

Zhang

Chen

et al. 2022

IJMS

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Hepatocellular carcinoma (HCC) is a common type of liver cancer and one of the highly lethal diseases worldwide. Hypoxia plays an important role in the development and prognosis of HCC. This study aimed to construct a new hypoxia-related prognosis signature and investigate its potential ceRNA axes in HCC. RNA profiles and hypoxia genes were downloaded, respectively, from the Cancer Genome Atlas hepatocellular carcinoma database and Gene Set Enrichment Analysis website. Cox regression analyses were performed to select the prognostic genes and construct the risk model. The ENCORI database was applied to build the lncRNA-miRNA–mRNA prognosis-related network. The TIMER and CellMiner databases were employed to analyze the association of gene expression in ceRNA with immune infiltration and drug sensitivity, respectively. Finally, the co-expression analysis was carried out to construct the potential lncRNA/miRNA/mRNA regulatory axes. We obtained a prognostic signature including eight hypoxia genes (ENO2, KDELR3, PFKP, SLC2A1, PGF, PPFIA4, SAP30, and TKTL1) and further established a hypoxia-related prognostic ceRNA network including 17 lncRNAs, six miRNAs, and seven mRNAs for hepatocellular carcinoma. Then, the analysis of immune infiltration and drug sensitivity showed that gene expression in the ceRNA network was significantly correlated with the infiltration abundance of multiple immune cells, the expression level of immune checkpoints, and drug sensitivity. Finally, we identified three ceRNA regulatory axes (SNHG1/miR-101-3p/PPFIA4, SNHG1/miR-101-3p/SAP30, and SNHG1/miR-101-3p/TKTL1) associated with the progression of HCC under hypoxia. Here, we constructed a prognosis gene signature and a ceRNA network related to hypoxia for hepatocellular carcinoma. Among the ceRNA network, six highly expressed lncRNAs (AC005540.1, AC012146.1, AC073529.1, AC090772.3, AC138150.2, AL390728.6) and one highly expressed mRNA (PPFIA4) were the potential biomarkers of hepatocellular carcinoma which we firstly reported. The three predicted hypoxia-related regulatory axes may play a vital role in the progression of hepatocellular carcinoma.

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Comprehensive biological function analysis of lncRNAs in hepatocellular carcinoma

Cited by 10 publications

References 120 publications

Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning

Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning

The lncRNA TERC promotes gastric cancer cell proliferation, migration, and invasion by sponging miR-423-5p to regulate SOX12 expression

Identification of Hypoxia-Related Prognostic Signature and Competing Endogenous RNA Regulatory Axes in Hepatocellular Carcinoma

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