The landscape of long noncoding RNA-involved and tumor-specific fusions across various cancers

Guo, Mengbiao; Xiao, Zhilong; Dai, Zhiming; Zhu, Ling; Lei, Hang; Diao, Li-Ting; Xiong, Yuanyan

doi:10.1093/nar/gkaa1119

Cited by 30 publications

(44 citation statements)

References 69 publications

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“…Numerous researches have documented that impaired lncRNA expression plays an indispensable role in tumorigenesis and development (35). In fact, several lncRNAs are up-regulated in tumors, where they reportedly promote tumor progression (36)(37)(38).…”

Section: Discussionmentioning

confidence: 99%

LncRNA FOXP4-AS1 Promotes Progression of Ewing Sarcoma and Is Associated With Immune Infiltrates

Xiong

et al. 2021

Front. Oncol.

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Ewing sarcoma (ES) is a highly malignant primary bone tumor with poor prognosis. Studies have shown that abnormal expression of lncRNA influences the prognosis of tumor patients. Herein, we established that FOXP4-AS1 was up-regulated in ES and this correlated with poor prognosis. Further analysis illustrated that FOXP4-AS1 down-regulation repression growth, migration, along with invasion of ES. On the contrary, up-regulation of FOXP4-AS1 promoted the growth, migration, as well as invasion of ES. To explore the mechanism of FOXP4-AS1, Spearman correlation analysis was carried out to determine genes that were remarkably linked to FOXP4-AS1 expression. The potential functions and pathways involving FOXP4-AS1 were identified by GO analysis, Hallmark gene set enrichment analysis, GSEA, and GSVA. The subcellular fractionation results illustrated that FOXP4-AS1 was primarily located in the cytoplasm of ES cells. Then a ceRNA network of FOXP4-AS1 was constructed. Analysis of the ceRNA network and GSEA yielded two candidate mRNAs for FOXP4-AS1. Results of the combined survival analysis led us to speculate that FOXP4-AS1 may affect the expression of TMPO by sponging miR-298, thereby regulating the malignant phenotype of ES. Finally, we found that FOXP4-AS1 may modulates the tumor immune microenvironment in an extracellular vesicle-mediated manner. In summary, FOXP4-AS1 correlates with poor prognosis of ES. It promotes the growth, migration, as well as invasion of ES cells and may modulate the tumor immune microenvironment.

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Section: Discussionmentioning

confidence: 99%

LncRNA FOXP4-AS1 Promotes Progression of Ewing Sarcoma and Is Associated With Immune Infiltrates

Xiong

et al. 2021

Front. Oncol.

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“…By integrating the DERs screened in previous steps, we constructed a ceRNA regulatory network and visualized the connection of genes using Cytoscape 3.6.1 software [ 21 ]. Functional analysis was performed using DAVID version 6.8 [ 22 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of Prognostic Factors in Cholangiocarcinoma Based on Integrated ceRNA Network Analysis

Jin

Liu

Xü

et al. 2022

Computational and Mathematical Methods in Medicine

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This study is aimed at screening prognostic biomarkers in cholangiocarcinoma (CHOL) based on competitive endogenous RNA (ceRNA) regulatory network analysis. Microarray data for lncRNAs, mRNA, and miRNAs were downloaded from the GEO and TCGA databases. Differentially expressed RNAs (DERs) were identified in CHOL and normal liver tissue samples. WGCNA was used to identify disease-related gene modules. By integrating the information from the starBase and DIANA-LncBasev2 databases, we constructed a ceRNA network. Survival analysis was performed, and a prognostic gene-based prognostic score (PS) model was generated. The correlation between gene expression and immune cell infiltration or immune-related feature genes was analyzed using TIMER. Finally, real-time quantitative PCR (RT-qPCR) was used to verify the expression of the 10 DERs with independent prognosis. A large cohort of DERs was identified in the CHOL and control samples. The ceRNA network consisted of 6 lncRNAs, 2 miRNAs, 90 mRNAs, and 98 nodes. Ten genes were identified as prognosis-related genes, and a ten-gene signature PS model was constructed, which exhibited a good prognosis predictive ability for risk assessment of CHOL patients (AUC value = 0.975). Four genes, ELF4, AGXT, ABCG2, and LDHD, were associated with immune cell infiltration and closely correlated with immune-related feature genes (CD14, CD163, CD33, etc.) in CHOL. Additionally, the consistency rate of the RT-qPCR results and bioinformatics analysis was 80%, implying a relatively high reliability of the bioinformatic analysis results. Our findings suggest that the ten-signature gene PS model has significant prognostic predictive value for patients with CHOL. These four immune-related DERs are involved in the progression of CHOL and may be useful prognostic biomarkers for CHOLs.

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“… 37 These transcripts regulate the expression of genes through affecting epigenetics, transcription, and translation, playing important physiological and pathological roles, and participating in various signaling pathways underlying multiple diseases. 38 LncRNAs are located in the nucleus or cytoplasm and regulate the expression of genes at the transcriptional or posttranscriptional level. LncRNAs in the nucleus regulate gene expression in various modes, such as isolating transcription factor/protein complexes from chromatin and gathering different proteins to form ribonucleoprotein complexes in response to stimuli.…”

Section: Significant Role Of Long Noncoding Rnas In Cerebral Ischemiamentioning

confidence: 99%

Emerging Role of LncRNAs in Ischemic Stroke—Novel Insights into the Regulation of Inflammation

Pan

Jiao

Wei

et al. 2021

JIR

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As a crucial kind of pervasive gene, long noncoding RNAs (lncRNAs) are abundant and key players in brain function as well as numerous neurological disorders, especially ischemic stroke. The mechanisms underlying ischemic stroke include angiogenesis, autophagy, apoptosis, cell death, and neuroinflammation. Inflammation plays a vital role in the pathological process of ischemic stroke, and systemic inflammation affects the patient's prognosis. Although a great deal of research has illustrated that various lncRNAs are closely relevant to regulate neuroinflammation and microglial activation in ischemic stroke, the specific interactional relationships and mechanisms between lncRNAs and neuroinflammation have not been described clearly. This review aimed to summarize the therapeutic effects and action mechanisms of lncRNAs on ischemia by regulating inflammation and microglial activation. In addition, we emphasize that lncRNAs have the potential to modulate inflammation by inhibiting and activating various signaling pathways, such as microRNAs, NF-κB and ERK.

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The landscape of long noncoding RNA-involved and tumor-specific fusions across various cancers

Cited by 30 publications

References 69 publications

LncRNA FOXP4-AS1 Promotes Progression of Ewing Sarcoma and Is Associated With Immune Infiltrates

LncRNA FOXP4-AS1 Promotes Progression of Ewing Sarcoma and Is Associated With Immune Infiltrates

Identification of Prognostic Factors in Cholangiocarcinoma Based on Integrated ceRNA Network Analysis

Emerging Role of LncRNAs in Ischemic Stroke—Novel Insights into the Regulation of Inflammation

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