Identification of Immune-Related lncRNA Pairs and Construction and Validation of a New Prognostic Signature of Colon Cancer

Xu, Minxian; Li, Qing; Zhang, Jianfang; Xie, Hui

doi:10.1155/2022/5827544

Cited by 7 publications

(6 citation statements)

References 40 publications

(39 reference statements)

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“…Among them, all ARLs are crucial in many ways. For instance, there is an association between WWC2-AS2 and the prognosis of multiple cancer types, such as LUAD [ 34 ], cervical cancer [ 35 ] and colon cancer [ 36 ]. Due to this, WWC2-AS2 is believed to be crucial to cancer development.…”

Section: Discussionmentioning

confidence: 99%

Molecular subgroup establishment and signature creation of lncRNAs associated with acetylation in lung adenocarcinoma

Chen,

Wang,

Shao

et al. 2024

Aging

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Background: The significance of long non-coding RNAs (lncRNAs) as pivotal mediators of histone acetylation and their influential role in predicting the prognosis of lung adenocarcinoma (LUAD) has been increasingly recognized. However, there remains uncertainty regarding the potential utility of acetylation-related lncRNAs (ARLs) in prognosticating the overall survival (OS) of LUAD specimens. Methods: The RNA-Seq and clinical information were downloaded from The Cancer Genome Atlas (TCGA). Through the differential analysis, weighted correlation network analysis (WGCNA), Pearson correlation test and univariate Cox regression, we found out the prognosis associated ARLs and divided LUAD specimens into two molecular subclasses. The ARLs were employed to construct a unique signature through the implementation of the Least Absolute Shrinkage and Selection Operator (LASSO) algorithm. Subsequently, the predictive performance was evaluated using ROC analysis and Kaplan-Meier survival curve analysis. Finally, ARL expression in LUAD was confirmed by quantitative real-time PCR (qRT-PCR). Results: We triumphantly built a ARLs prognostic model with excellent predictive accuracy for LUAD. Univariate and multivariate Cox analysis illustrated that risk model served as an independent predictor for influencing the overall survival OS of LUAD. Furthermore, a nomogram exhibited strong prognostic validity. Additionally, variations were observed among subgroups in the field of immunity, biological functions, drug sensitivity and gene mutations within the field. Conclusions: Nine ARLs were identified as promising indicators of personalized prognosis and drug selection for people suffering with LUAD.

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Section: Discussionmentioning

confidence: 99%

Molecular subgroup establishment and signature creation of lncRNAs associated with acetylation in lung adenocarcinoma

Chen,

Wang,

Shao

et al. 2024

Aging

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“…Moreover, the expression of WWC2-AS2 was corrected based on the in ltration level of immune cell subtypes [22] . Furthermore, Xu et al indicated that WWC2-AS2|AL355916.2, an immune-related long non-coding ribonucleic acid gene pair pattern in colon cancer, related to the survival outcome, clinicopathological characteristics of prognosis of colon cancer [23] . Thus, WWC2-AS2 could be used as a biomarker and therapeutic target for patients with PTC.…”

Section: Discussionmentioning

confidence: 99%

Long non-coding RNA AC005479.2 plays a critical role in papillary thyroid carcinoma

Liang¹,

Liu²,

Wang³

et al. 2023

Preprint

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Background Papillary thyroid carcinoma (PTC) is the most common subtype of differentiated thyroid malignancy, with increasing incidence. The long non-coding RNA (lncRNA) AC005479.2 has been shown to play a role in the tumorigenesis and development of multiple cancers, although its role in PTC remains unclear. Therefore, we aimed to identify the expression, function, and mechanisms of AC005479.2 in PTC. Methods The data were downloaded from TCGA database. The expression of AC005479.2 in PTC samples was determined by R package “limma” and RT-qPCR, and weighted gene co-expression network analysis (WGCNA) was used to explore the association between AC005479.2 and PTC. Through genetic enrichment analysis (GSEA) set of AC005479.2, potential function and molecular mechanism were discussed. Receiver operating characteristic (ROC) curve analysis was used to determine the performance of AC005479.2. Univariate and multivariate Cox regression analyses were used to analyze the effects on the prognosis of patients with PTC. Results The results showed that AC005479.2 was up-regulated in TCGA-PTC and PTC samples. Eleven PTC-related modules were obtained from the WGCNA, and AC005479.2 was in the blue module, which had the strongest association with PTC. AC005479.2-related genes were obtained from the blue module, and GSEA-GO analysis of these genes was mainly enriched in aerobic respiration, lipid oxidation, and negative regulation of extrinsic apoptotic signaling pathway via death down, while KEGG analysis was mainly enriched in the MAPK, JAK-STAT, and NOTCH signaling pathways. Area under the ROC curve is 0.838, prompt AC005479.2 may be PTC diagnostic biomarkers. Univariate and multivariate Cox analyses indicated that AC005479.2 was an independent risk factor for the prognosis of patients with PTC. Conclusion AC005479.2 is up-regulated in PTC, where it may serve as a biomarker gene, providing an important basis for future research.

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“…The prognostic value of immune-related lncRNAs has been found in various cancers. Currently, a prognostic model has been conducted based on eight immune-related lncRNAs pairs that can effectively predict the prognosis of patients with COAD ( 69 ). Here, we performed an in-depth analysis of the relationship between the risk model and the distribution of immune-infiltrating cells by ImmuCellAI.…”

Section: Discussionmentioning

confidence: 99%

Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinoma

Zhang

et al. 2022

Front. Oncol.

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PurposeColon adenocarcinoma (COAD) is the most common type of colorectal cancer (CRC) and is associated with poor prognosis. Emerging evidence has demonstrated that glycosylation by long noncoding RNAs (lncRNAs) was associated with COAD progression. To date, however, the prognostic values of glycosyltransferase (GT)-related lncRNAs in COAD are still largely unknown.MethodsWe obtained the expression matrix of mRNAs and lncRNAs in COAD from The Cancer Genome Atlas (TCGA) database. Then, the univariate Cox regression analysis was conducted to identify 33 prognostic GT-related lncRNAs. Subsequently, LASSO and multivariate Cox regression analysis were performed, and 7 of 33 GT-related lncRNAs were selected to conduct a risk model. Gene set enrichment analysis (GSEA) was used to analyze gene signaling pathway enrichment of the risk model. ImmuCellAI, an online tool for estimating the abundance of immune cells, and correlation analysis were used to explore the tumor-infiltrating immune cells in COAD. Finally, the expression levels of seven lncRNAs were detected in colorectal cancer cell lines by reverse transcription-quantitative polymerase chain reaction (RT-qPCR).ResultsA total of 1,140 GT-related lncRNAs were identified, and 7 COAD-specific GT-related lncRNAs (LINC02381, MIR210HG, AC009237.14, AC105219.1, ZEB1-AS1, AC002310.1, and AC020558.2) were selected to conduct a risk model. Patients were divided into high- and low-risk groups based on the median of risk score. The prognosis of the high-risk group was worse than that of the low-risk group, indicating the good reliability and specificity of our risk model. Additionally, a nomogram based on the risk score and clinical traits was built to help clinical decisions. GSEA showed that the risk model was significantly enriched in metabolism-related pathways. Immune infiltration analysis revealed that five types of immune cells were significantly different between groups, and two types of immune cells were negatively correlated with the risk score. Besides, we found that the expression levels of these seven lncRNAs in tumor cells were significantly higher than those in normal cells, which verified the feasibility of the risk model.ConclusionThe efficient risk model based on seven GT-related lncRNAs has prognostic potential for COAD, which may be novel biomarkers and therapeutic targets for COAD patients.

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Identification of Immune-Related lncRNA Pairs and Construction and Validation of a New Prognostic Signature of Colon Cancer

Cited by 7 publications

References 40 publications

Molecular subgroup establishment and signature creation of lncRNAs associated with acetylation in lung adenocarcinoma

Molecular subgroup establishment and signature creation of lncRNAs associated with acetylation in lung adenocarcinoma

Long non-coding RNA AC005479.2 plays a critical role in papillary thyroid carcinoma

Glycosyltransferase-related long non-coding RNA signature predicts the prognosis of colon adenocarcinoma

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