Identification of Potential Biomarkers of Prognosis-Related Long Non-Coding RNA (lncRNA) in Pediatric Rhabdoid Tumor of the Kidney Based on ceRNA Networks

Wu, Xian; Liu, Jie; Zhu, Chunhui; Ma, Mingdi; Chen, Xin; Liu, Yusheng; Xia, Nan; Dong, Qi

doi:10.12659/msm.927725

Cited by 10 publications

(5 citation statements)

References 24 publications

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“…These data suggest that the lncRNA–mRNA pair MIR210HG–BPIFC and its regulatory miRNAs play specific roles in HCM, different from their roles in tumor conditions. Additionally, Wu et al found that ZNF503-AS2 could be used as an independent prognostic biomarker for rhabdoid tumors of the kidney through univariate and multivariate Cox analyses [ 30 ]. Furthermore, prognostic and diagnostic models for kidney renal clear-cell carcinoma suggested that ZNF503-AS2 could be used as a prognostic and diagnostic biomarker in patients [ 31 ], since we found that the expression levels of this candidate lncRNA in the ceRNA network were significantly dysregulated in HCM patients.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analyses and Experimental Validation Identified Immune-Related lncRNA–mRNA Pair MIR210HG–BPIFC Regulating the Progression of Hypertrophic Cardiomyopathy

Zhang,

Zhao,

Jin

et al. 2024

IJMS

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Hypertrophic cardiomyopathy (HCM) is a disease in which the myocardium of the heart becomes asymmetrically thickened, malformed, disordered, and loses its normal structure and function. Recent studies have demonstrated the significant involvement of inflammatory responses in HCM. However, the precise role of immune-related long non-coding RNAs (lncRNAs) in the pathogenesis of HCM remains unclear. In this study, we performed a comprehensive analysis of immune-related lncRNAs in HCM. First, transcriptomic RNA-Seq data from both HCM patients and healthy individuals (GSE180313) were reanalyzed thoroughly. Key HCM-related modules were identified using weighted gene co-expression network analysis (WGCNA). A screening for immune-related lncRNAs was conducted within the key modules using immune-related mRNA co-expression analysis. Based on lncRNA–mRNA pairs that exhibit shared regulatory microRNAs (miRNAs), we constructed a competing endogenous RNA (ceRNA) network, comprising 9 lncRNAs and 17 mRNAs that were significantly correlated. Among the 26 lncRNA–mRNA pairs, only the MIR210HG–BPIFC pair was verified by another HCM dataset (GSE130036) and the isoprenaline (ISO)-induced HCM cell model. Furthermore, knockdown of MIR210HG increased the regulatory miRNAs and decreased the mRNA expression of BPIFC correspondingly in AC16 cells. Additionally, the analysis of immune cell infiltration indicated that the MIR210HG–BPIFC pair was potentially involved in the infiltration of naïve CD4+ T cells and CD8+ T cells. Together, our findings indicate that the decreased expression of the lncRNA–mRNA pair MIR210HG–BPIFC was significantly correlated with the pathogenesis of the disease and may be involved in the immune cell infiltration in the mechanism of HCM.

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Section: Discussionmentioning

confidence: 99%

Transcriptomic Analyses and Experimental Validation Identified Immune-Related lncRNA–mRNA Pair MIR210HG–BPIFC Regulating the Progression of Hypertrophic Cardiomyopathy

Zhang,

Zhao,

Jin

et al. 2024

IJMS

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“…Previous studies have indicated that the three biomarkers identified in the present study were related to OS in other cancers. For example, Wu et al (2020 ) found that ZNF503-AS2 could be used as an independent prognostic biomarker for rhabdoid tumors of the kidney by univariate and multivariate Cox analyses. Xing et al (2021 ) found that LINC02609 was associated with the OS of patients with KIRC.…”

Section: Discussionmentioning

confidence: 99%

Establishment of a prognostic ferroptosis- and immune-related long noncoding RNAs profile in kidney renal clear cell carcinoma

et al. 2022

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Background: Ferroptosis and immunity are novel treatments that target several cancers, including kidney renal clear cell carcinoma (KIRC). Long noncoding RNAs (lncRNAs) are an important class of gene expression regulators that play fundamental roles in the regulation of ferroptosis and immunity. We aimed to identify ferroptosis- and immune-related lncRNAs as biomarkers in patients with KIRC.Methods: Corresponding data for each patient with KIRC were obtained from The Cancer Genome Atlas (TCGA) database. Univariate and multivariate Cox regression analyses were used to identify candidate biomarkers followed by least absolute shrinkage and selection operator (LASSO) regression analyses, weighted gene coexpression network analysis (WGCANA), and gene set enrichment analysis (GSEA).Results: Three ferroptosis- and immune-related differentially expressed lncRNAs (FI-DELs) (AC124854.1, LINC02609, and ZNF503-AS2) were markedly and independently correlated with the overall survival (OS) of patients with KIRC. The area under the curve (AUC) value of the prognostic model in the entire group using the three FI-DELs was > 0.70. The sensitivity and specificity of the diagnostic model using the three FI-DELs were 0.8586 and 0.9583, respectively.Conclusion: The present study found that AC124854.1, LINC02609, and ZNF503-AS2 were considerably and independently correlated with the OS of patients with KIRC, suggesting that the three FI-DELs could be used as prognostic and diagnostic biomarkers for patients with KIRC.

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“…In addition, downregulated LOC100130691 is associated with worse relapse-free survival and overall survival in patients with basal breast cancer ( 34 ). ZNF503-AS2 was associated with a high risk of death in pediatric rhabdoid tumor of the kidney ( 35 ). The enrichment analysis revealed that the lncRNAs were involved in highly associated cancer pathways such as cell–cell adhesion and Wnt signaling pathway.…”

Section: Discussionmentioning

confidence: 99%

lncRNA pair as candidate diagnostic signature for colorectal cancer based on the within-sample relative expression levels

Wang

Shi

et al. 2022

Front. Oncol.

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BackgroundEarly diagnosis of colorectal cancer could significantly improve the prognosis and reduce mortality. However, indeterminate diagnosis is often met in pathology diagnosis in biopsy samples. Abnormal expression of long non-coding RNA (lncRNA) is associated with the initiation and progression of colorectal cancer. It is of great value and clinical significance to explore lncRNAs as candidate diagnostic biomarkers in colorectal cancer.MethodsBased on the within-sample relative expression levels of lncRNA pairs, we identified a group of candidate diagnostic biomarkers for colorectal cancer. In addition, we validated it in independent datasets produced by different laboratories and different platforms. We also tested it in colorectal cancer tissue samples using quantitative real-time polymerase chain reaction (RT-qPCR).ResultsA biomarker consisting of six lncRNA pairs including nine lncRNAs was identified for the diagnosis of colorectal cancer. For a total of 950 cancer samples and 247 non-cancer samples, both of the sensitivity and specificity could achieve approximately 90%. For adenoma samples, the accuracy could achieve 73%. For normal tissues from inflammatory bowel disease patients, 93% (14/15) were correctly classified as non-cancer. Furthermore, the lncRNA pair biomarker showed excellent performance in all clinical stages; even in the early stage, the accuracy could achieve 87% and 82% in stage I and II. Meanwhile, the biomarker was also robust to the microsatellite instability status. More importantly, we measured the biomarker in 35 colorectal cancer and 30 cancer-adjacent tissue samples using quantitative real-time polymerase chain reaction (RT-qPCR). The accuracy could achieve 93.3% (70/75). Specially, even in early-stage tumors (I and II), the accuracy could also achieve 90.9% (30/33). The enrichment analysis revealed that these lncRNAs were involved in highly associated cancer pathways and immune-related pathways. Immune analysis showed that these marker lncRNAs were associated with multiple immune cells, implying that they might be involved in the regulation of immune cell functions in colorectal cancer. Most of the biomarker lncRNAs were also differentially expressed between the mutant group and wild-type group of colorectal cancer driver genes.ConclusionWe identified and validated six lncRNA pairs including nine lncRNAs as a biomarker for assisting in the diagnosis of colorectal cancer.

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Identification of Potential Biomarkers of Prognosis-Related Long Non-Coding RNA (lncRNA) in Pediatric Rhabdoid Tumor of the Kidney Based on ceRNA Networks

Cited by 10 publications

References 24 publications

Transcriptomic Analyses and Experimental Validation Identified Immune-Related lncRNA–mRNA Pair MIR210HG–BPIFC Regulating the Progression of Hypertrophic Cardiomyopathy

Transcriptomic Analyses and Experimental Validation Identified Immune-Related lncRNA–mRNA Pair MIR210HG–BPIFC Regulating the Progression of Hypertrophic Cardiomyopathy

Establishment of a prognostic ferroptosis- and immune-related long noncoding RNAs profile in kidney renal clear cell carcinoma

lncRNA pair as candidate diagnostic signature for colorectal cancer based on the within-sample relative expression levels

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