The Risk Correlation between N7-Methylguanosine Modification-Related lncRNAs and Survival Prognosis of Oral Squamous Cell Carcinoma Based on Comprehensive Bioinformatics Analysis

Xu, Yanglong; Zhang, Xue; Mei, Jie

doi:10.1155/2022/1666792

Cited by 5 publications

(5 citation statements)

References 45 publications

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“…Although some differentially expressed genes were shared between T2D and control samples ( Figure 3 B), 181 up- and 179 down-regulated genes were differentially regulated specifically in T2D compared to the control samples, including 35 up- and 22 down-regulated lncRNA genes ( Supplementary Table S6 ). Among these up-regulated lncRNA genes, only the following nine have been previously studied: (1) ENSG00000232855 (novel transcript) [ 75 ]; (2) ENSG00000272512 (novel transcript) [ 76 ]; (3) KCNJ2 antisense RNA 1 (KCNJ2-AS1) [ 77 , 78 , 79 ]; (4) KLHDC7B divergent transcript (KLHDC7B-DT) [ 80 , 81 , 82 ]; (5) long intergenic non-protein-coding RNA 2015 (LINC02015) [ 83 , 84 ]; (6) long intergenic non-protein-coding RNA 2381 (LINC02381) [ 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 ]; (7) long intergenic non-protein-coding RNA 2541 (LINC02541) [ 94 ]; (8) serpin family B member 9 pseudogene 1 (SERPINB9P1) [ 95 , 96 , 97 ]; and (9) USP30 antisense RNA 1 (USP30-AS1) [ 98 , 99 , 100 ]. However, only the functions of the lncRNA genes LINC02381 and USP30_AS1 are known, with the former known to bind transcription factors [ 85 ], RNA-binding proteins [ 86 ], and miRNAs [ 87 , 88 , 89 , 90 , 91 , 92 , 93 ]; while USP30-AS1 acts as a miRNA sponge [ 98 , 99 ] and is involved in the cis-regulation of the nearby protein-coding genes USP30 and ANKRD13A [ 100 ].…”

Section: Resultsmentioning

confidence: 99%

“…(2) ENSG00000272512 (novel transcript) [76]; (3) KCNJ2 antisense RNA 1 (KCNJ2-AS1) [77][78][79]; (4) KLHDC7B divergent transcript (KLHDC7B-DT) [80][81][82]; (5) long intergenic non-proteincoding RNA 2015 (LINC02015) [83,84]; (6) long intergenic non-protein-coding RNA 2381 (LINC02381) [85][86][87][88][89][90][91][92][93]; (7) long intergenic non-protein-coding RNA 2541 (LINC02541) [94]; (8) serpin family B member 9 pseudogene 1 (SERPINB9P1) [95][96][97]; and (9) USP30 antisense RNA 1 (USP30-AS1) [98][99][100]. However, only the functions of the lncRNA genes LINC02381 and USP30_AS1 are known, with the former known to bind transcription factors [85], RNA-binding proteins [86], and miRNAs [87][88][89][90][91][92][93]; while USP30-AS1 acts as a miRNA sponge [98,99] and is involved in the cis-regulation of the nearby protein-coding genes USP30 and ANKRD13A [100].…”

Section: Many Lncrnas Are Differentially Expressed In Cultured Macrop...mentioning

confidence: 99%

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T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes

Distefano

Ilieva

Madsen

et al. 2023

ncRNA

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Type II diabetes (T2D) is a growing health problem worldwide due to increased levels of obesity and can lead to other life-threatening diseases, such as cardiovascular and kidney diseases. As the number of individuals diagnosed with T2D rises, there is an urgent need to understand the pathogenesis of the disease in order to prevent further harm to the body caused by elevated blood glucose levels. Recent advances in long non-coding RNA (lncRNA) research may provide insights into the pathogenesis of T2D. Although lncRNAs can be readily detected in RNA sequencing (RNA-seq) data, most published datasets of T2D patients compared to healthy donors focus only on protein-coding genes, leaving lncRNAs to be undiscovered and understudied. To address this knowledge gap, we performed a secondary analysis of published RNA-seq data of T2D patients and of patients with related health complications to systematically analyze the expression changes of lncRNA genes in relation to the protein-coding genes. Since immune cells play important roles in T2D, we conducted loss-of-function experiments to provide functional data on the T2D-related lncRNA USP30-AS1, using an in vitro model of pro-inflammatory macrophage activation. To facilitate lncRNA research in T2D, we developed a web application, T2DB, to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in T2D patients compared to healthy donors or subjects without T2D.

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Section: Resultsmentioning

confidence: 99%

Section: Many Lncrnas Are Differentially Expressed In Cultured Macrop...mentioning

confidence: 99%

T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes

Distefano

Ilieva

Madsen

et al. 2023

ncRNA

View full text Add to dashboard Cite

show abstract

“…Further evidence suggests that FENDRR acts as a miRNA sponge for miR-214-3p, thereby suppressing the progression of gastric cancer [23]. Moreover, AL513550.1 has been implicated in elucidating the link between survival prognosis and N7-methylguanosine modification-related lncRNAs in oral squamous cell carcinoma [24]. Similarly, ATP2A1-AS1 has emerged as a promising prognostic biomarker for patients with cervical cancer [25].…”

Section: Discussionmentioning

confidence: 99%

Analysis of disulfidptosis‐ and cuproptosis‐related LncRNAs in modulating the immune microenvironment and chemosensitivity in colon adenocarcinoma

Fan,

Wu,

Chen

et al. 2024

IET Systems Biology

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The main objective was to establish a prognostic model utilising long non‐coding RNAs associated with disulfidptosis and cuproptosis. The data for RNA‐Sequence and clinicopathological information of Colon adenocarcinoma (COAD) were acquired from The Cancer Genome Atlas. A prognostic model was constructed using Cox regression and the Least Absolute Shrinkage and Selection Operator method. The model's predictive ability was assessed through principal component analysis, Kaplan–Meier analysis, nomogram etc. The ability of identifying the rates of overall survival, infiltration of immune cells, and chemosensitivity was also explored. In vitro experiments were conducted for the validation of differential expression and function of lncRNAs. A disulfidptosis and cuproptosis‐related lncRNA prognostic model was constructed. The prognostic model exhibits excellent independent predictive capability for patient outcomes. Based on the authors’ model, the high‐risk group exhibited higher tumour mutation burdened worse survival. Besides, differences in immune cell infiltration and responsiveness to chemotherapeutic medications exist among patients with different risk scores. Furthermore, aberrant expressions in certain lncRNAs have been validated in HCT116 cells. In particular, FENDRR and SNHG7 could affect the proliferation and migration of colorectal cancer cells. Our study developed a novel prognostic signature, providing valuable insights into prognosis, immune infiltration, and chemosensitivity in COAD patients.

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“…Despite the application of multimodal treatment including surgery, radiation therapy, chemotherapy, targeted molecular therapy, and immunotherapy, the 5-year survival rate is still relatively low [15]. A previous study reported that AC005332.6 was an independent prognostic factor for oral squamous cell carcinoma based on bio-informatics analysis [22]. Additionally, LINC02747 had been explored to play an essential role in clear cell renal cell carcinoma (ccRCC).…”

Section: Discussionmentioning

confidence: 99%

Construction of a cuproptosis-related lncRNA signature as a novel prognostic model for pancreatic adenocarcinoma

Zheng

et al. 2022

Preprint

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Background Pancreatic adenocarcinoma (PAAD) is one of the common malignant tumors, with high mortality and poor prognosis. Long non-coding RNA (lncRNA) plays a vital role in the progression of tumors. Cuproptosis, a newly identified form of programmed cell death, is thought to play a role in tumorigenesis. However, the role and prognostic value of cuproptosis-related lncRNA in PAAD remains unknown. Therefore, our study is to construct the role of cuproptosis-related lncRNA signature for predicting the prognosis of PAAD patients. Material and methods The mRNAs and lncRNAs expression profiles and clinical data of PAAD were obtained from The Cancer Genome Atlas (TCGA) databases. The prognosis signature was constructed by least absolute shrinkage and selection operator (LASSO) regression and Cox regression analysis. Patients were separated into high and low risk groups according to the median score. Using Kaplan-Meier, Concordance index (C-index), area under the receiver operating characteristic (ROC) curves to assess prognostic ability of the signature. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes Enrichment (KEGG), immune-related functions, and tumor mutation burden (TMB) were analyzed based on the signature. The likelihood of an immunotherapy response was estimated using tumor immune dysfunction and exclusion (TIDE) algorithms. PRRophetic package was used to identify its sensitivity toward potential drugs for PAAD. Results In total, we obtained 4 cuproptosis-related lncRNAs and constructed a prognostic signature. High-risk patients were correlated with worse overall survival (OS) and progression-free survival (PFS) and higher mortality. Multivariate Cox regression was performed to identify independent risk factor poor prognosis of high risk scores. ROC, C-index, and nomogram also showed the signature can accurately predict the prognosis of patients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the biological functions of lncRNAs are associated with tumor development, especially immune response. Tumor Mutation Burden (TMB) and Tumor Immune Dysfunction and Exclusion (TIDE) scores were significantly different between high- and low-risk groups. The three drugs, including Paclitaxel, Gefitinib, and 17-AAG, were more sensitive in the high-risk group. Conclusion The 4 cuproptosis-related lncRNAs signature accurately predicted the prognosis of PAAD and led to better prognosis and treatment options for patients.

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The Risk Correlation between N7-Methylguanosine Modification-Related lncRNAs and Survival Prognosis of Oral Squamous Cell Carcinoma Based on Comprehensive Bioinformatics Analysis

Cited by 5 publications

References 45 publications

T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes

T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes

Analysis of disulfidptosis‐ and cuproptosis‐related LncRNAs in modulating the immune microenvironment and chemosensitivity in colon adenocarcinoma

Construction of a cuproptosis-related lncRNA signature as a novel prognostic model for pancreatic adenocarcinoma

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