Integrated Analysis of the Functions and Prognostic Values of RNA-Binding Proteins in Colorectal Cancer

Wang, Ya; Chen, Yuqiao; Xiao, Shuai; Fu, Kai

doi:10.3389/fcell.2020.595605

Cited by 5 publications

(3 citation statements)

References 76 publications

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“…Recently, a Cox model based on seven RBPs was reported to predict the survival of patients with COAD, two of which (PPARGC1A and LRRFIP2) were also present in our model ( 36 ). Among the five RBPs in our model, the other three genes (CELF4, NOP14, ZNF385A) were not previously reported to be associated with COAD.…”

Section: Conclusion and Discussionmentioning

confidence: 93%

A New RBPs-Related Signature Predicts the Prognosis of Colon Adenocarcinoma Patients

2021

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The dysregulation of RNA binding proteins (RBPs) is closely related to tumorigenesis and development. However, the role of RBPs in Colon adenocarcinoma (COAD) is still poorly understood. We downloaded COAD’s RNASeq data from the Cancer Genome Atlas (TCGA) database, screened the differently expressed RBPs in normal tissues and tumor, and constructed a protein interaction network. COAD patients were randomly divided into a training set (N = 315) and a testing set (N = 132). In the training set, univariate Cox analysis identified 12 RBPs significantly related to the prognosis of COAD. By multivariate COX analysis, we constructed a prognostic model composed of five RBPs (CELF4, LRRFIP2, NOP14, PPARGC1A, ZNF385A) based on the lowest Akaike information criterion. Each COAD patient was scored according to the model formula. Further analysis showed that compared with the low-risk group, the overall survival rate (OS) of patients in the high-risk group was significantly lower. The area under the curve of the time-dependent receiver operator characteristic (ROC) curve was 0.722 in the training group and 0.738 in the test group, which confirmed a good prediction feature. In addition, a nomogram was constructed based on clinicopathological characteristics and risk scores. C-index and calibration curve proved the accuracy in predicting the 1-, 3-, and 5-year survival rates of COAD patients. In short, we constructed a superior prognostic and diagnostic signature composed of five RBPs, which indicates new possibilities for individualized treatment of COAD patients.

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Section: Conclusion and Discussionmentioning

confidence: 93%

A New RBPs-Related Signature Predicts the Prognosis of Colon Adenocarcinoma Patients

2021

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“…AFF3, among other RNA-binding proteins, has been investigated in CRC. Downregulation of AFF3 has been detected in CRC and is associated with poor prognosis [28]. Further experimental validation is required to prove the regulation of these genes by nov-miR-3345-5p and nov-miR-13172-3p in colorectal tumors.…”

Section: Discussionmentioning

confidence: 99%

Discovery of Novel miRNAs in Colorectal Cancer: Potential Biological Roles and Clinical Utility

Minutentag,

Seneda,

Barros-Filhos

et al. 2023

ncRNA

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Deregulated miRNAs are associated with colorectal cancer (CRC), with alterations depending on the tumor location. Novel tissue-specific miRNAs have been identified in different tumors and are associated with cancer. We used miRMaster to identify novel miRNAs in CRC from the TCGA and GEO data (discovery and validation groups). We used TCGA data from five tissues to analyze miRNA tissue specificity. miRDB was used to predict miRNA targets, and the UCSC Xena Browser was used to evaluate target expression. After successive analyses, we identified 15 novel miRNAs with the same expression patterns in CRC in both the discovery and validation groups. Four molecules (nov-miR-13844-5p, nov-miR-7154-5p, nov-miR-5035-3p, and nov-miR-590-5p) were differentially expressed in proximal and distal CRC. The nov-miR-3345-5p and nov-miR-13172-3p, which are upregulated in tumors, are only expressed in colorectal tissues. These molecules have been linked to a worse prognosis in right-sided colon and rectal carcinomas. An analysis revealed an association between eight novel miRNAs and 81 targets, mostly cancer-related genes, with varying expression based on tumor location. These findings provide new miRNAs with potential biological relevance, molecular biomarkers, and therapeutic targets for CRC treatment.

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“…To date, exosomal gene-based diagnostic models have not been described for CRC, although considerable efforts have been made to develop prognostic signatures based on differentially expressed genes (Chen et al, 2019;Dai et al, 2020;Wang et al, 2020). The present study analyzed differences in exosomal gene expression between CRC patients and healthy humans.…”

Section: Discussionmentioning

confidence: 99%

A Diagnostic Model Using Exosomal Genes for Colorectal Cancer

et al. 2022

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Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Exosomes have great potential as liquid biopsy specimens due to their presence and stability in body fluids. However, the function and diagnostic values of exosomal genes in CRC are poorly understood. In the present study, exosomal data of CRC and healthy samples from the exoRBase 2.0 and Gene Expression Omnibus (GEO) databases were used, and 38 common exosomal genes were identified. Through the least absolute shrinkage and selection operator (Lasso) analysis, support vector machine recursive feature elimination (SVM-RFE) analysis, and logistic regression analysis, a diagnostic model of the training set was constructed based on 6 exosomal genes. The diagnostic model was internally validated in the test and exoRBase 2.0 database and externally validated in the GEO database. In addition, the co-expression analysis was used to cluster co-expression modules, and the enrichment analysis was performed on module genes. Then a protein–protein interaction and competing endogenous RNA network were constructed and 10 hub genes were identified using module genes. In conclusion, the results provided a comprehensive understanding of the functions of exosomal genes in CRC as well as a diagnostic model related to exosomal genes.

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Integrated Analysis of the Functions and Prognostic Values of RNA-Binding Proteins in Colorectal Cancer

Cited by 5 publications

References 76 publications

A New RBPs-Related Signature Predicts the Prognosis of Colon Adenocarcinoma Patients

A New RBPs-Related Signature Predicts the Prognosis of Colon Adenocarcinoma Patients

Discovery of Novel miRNAs in Colorectal Cancer: Potential Biological Roles and Clinical Utility

A Diagnostic Model Using Exosomal Genes for Colorectal Cancer

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