Integrated analysis of RNA-binding proteins in human colorectal cancer

Fan, Xuehui; Liu, Huan; Shi, You; Guo, Fanghan; Wang, Haining; Zhao, Xueping; Zhong, Di; Li, Guozhong

doi:10.1186/s12957-020-01995-5

Cited by 25 publications

(18 citation statements)

References 79 publications

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“…Expression of LINC01224 and MYO6 in colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ) was provided via The Cancer Genome Atlas (TCGA) database ( http://www.cancer.gov/tcga ) [ 25 ]. The binding sites of YY1 and LINC01224 promoter were predicted via JASPAR algorithms ( http://jaspar.genereg.net /) [ 26 ].…”

Section: Methodsmentioning

confidence: 99%

LINC01224 promotes colorectal cancer progression through targeting miR-485-5p/MYO6 axis

Dong

Wang

et al. 2021

World J Surg Onc

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Background Long noncoding RNAs (lncRNAs) are related to colorectal cancer (CRC) development. However, the role and mechanism of lncRNA LINC01224 in CRC development are largely unknown. Methods LINC01224, Yin Yang 1 (YY1), microRNA (miR)-485-5p, and myosins of class VI (MYO6) levels were examined using quantitative reverse transcription polymerase chain reaction and western blotting. Functional analyses were processed through CCK-8, colony formation, flow cytometry, transwell, and xenograft analyses. Dual-luciferase reporter, chromatin immunoprecipitation (ChIP), RNA immunoprecipitation, and pull-down assays were conducted to analyze the binding interaction. Results LINC01224 abundance was elevated in CRC tissue samples and cell lines. Elevated LINC01224 might indicate the lower 5-year overall survival in 52 CRC patients. LINC01224 was upregulated via the transcription factor YY1. LINC01224 knockdown restrained CRC cell proliferation, migration, and invasion and increased apoptosis. MiR-485-5p was sponged by LINC01224, and miR-485-5p downregulation relieved the influence of LINC01224 interference on CRC progression. MYO6 was targeted via miR-485-5p and regulated via LINC01224/miR-485-5p axis. MiR-485-5p overexpression suppressed CRC cell proliferation, migration, and invasion and facilitated apoptosis. MYO6 upregulation mitigated the role of miR-485-5p. LINC01224 knockdown decreased xenograft tumor growth. Conclusion YY1-induced LINC01224 regulates CRC development via modulating miR-485-5p/MYO6 axis.

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Section: Methodsmentioning

confidence: 99%

LINC01224 promotes colorectal cancer progression through targeting miR-485-5p/MYO6 axis

Dong

Wang

et al. 2021

World J Surg Onc

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“…Given that RBPs are critical regulators and effectors of cancer, they also should be regarded as hallmarks and potential targets for early diagnosis, prognosis and clinical intervention of cancer. NOP14/MRPS23/POP1 exhibit prognostic value in colorectal cancer, while APOBEC3C/DCAF13/EIF4E3/EZR possess significance in predicting prognosis of breast cancer (17,18). Moreover, the Ribavirin, an antiviral guanosine analog, is able to slacken tumorigenesis by competitively interacting with the 5'-Cap of eIF4E mRNA, subsequently impeding the translation and transposition of eIF4E-regualted Cyclin D1 (19).…”

Section: Introductionmentioning

confidence: 99%

Identification of a Three-RNA Binding Proteins (RBPs) Signature Predicting Prognosis for Breast Cancer

Liu

Sun

et al. 2021

Front. Oncol.

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BackgroundTo date, breast cancer remains the primary cause of tumor-related death among women, even though some leap-type developments of oncology have been done to slash the mortality. Considering the tumor heterogeneity and individual variation, the more reliable biomarkers are required to be identified for supporting the development of precision medicine in breast cancer.MethodsBased on the TCGA-BRCA and METABRIC databases, the differently expressed RNA binding proteins (RBPs) between tumor and normal tissues were investigated. In this study, we focused on the communal differently expressed RBPs in four subtypes of breast cancer. Lasso-penalized Cox analysis, Stepwise-multivariate Cox analysis and Kaplan–Meier survival curve were performed to identify the hub RBP-coding genes in predicting prognosis of breast cancer, and a prognostic model was established. The efficiency of this model was further validated in other independent GSE20685, GSE4922 and FUSCC-TNBC cohorts by calculating the risk score and performing survival analysis, ROC and nomogram. Moreover, pathologic functions of the candidate RBPs in breast cancer were explored using some routine experiments in vitro, and the potential compounds targeting these RBPs were predicted by reviewing the Comparative Toxicogenomics Database.ResultsHere, we identified 62 RBPs which were differently expressed between the tumor and normal tissues. Thereinto, three RBPs (MRPL12, MRPL13 and POP1) acted as independent risk factors, and their expression pattern also correlated with poor prognosis of patients. A prognostic model, built with these 3-RBPs, possessed statistical significance to predict the survival probability of patients with breast cancer. Furthermore, experimental validations showed that down-regulating the expression of endogenous MRPL12, MRPL13 or POP1 could dramatically suppress the cellular viability and migration of breast cancer cells in vitro. Besides, some compounds (such as the Acetaminophen, Urethane and Tunicamycin) were predicted for curing breast cancer via targeting MRPL12, MRPL13 and POP1 simultaneously.ConclusionThis study identified and established a 3-RBPs-based signature and nomogram for predicting the survival probability of patients with breast cancer. MRPL12, MRPL13 and POP1 might act as oncogenes in maintaining cellular viability and accelerating metastasis of breast cancer cells, implying the possibility of which to be designed as biomarkers and/or therapeutic targets for breast cancer.

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“…However, RBPs regulate CRC progression through poorly understood mechanisms. Previous studies have shown that twelve identified RBPs may be promising predictors of CRC but no further verification at the protein expression level ( Fan et al, 2020 ). Zhang et al (2020) was constructed a prognostic risk score model based on four RBPs and explore their prognosis value for CRC patients.…”

Section: Introductionmentioning

confidence: 99%

Construction and validation of an RNA-binding protein-associated prognostic model for colorectal cancer

Miao

Zhang²,

Su³

et al. 2021

PeerJ

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Colorectal cancer (CRC) is one of the most prevalent and fatal malignancies, and novel biomarkers for the diagnosis and prognosis of CRC must be identified. RNA-binding proteins (RBPs) are essential modulators of transcription and translation. They are frequently dysregulated in various cancers and are related to tumorigenesis and development. The mechanisms by which RBPs regulate CRC progression are poorly understood and no clinical prognostic model using RBPs has been reported in CRC. We sought to identify the hub prognosis-related RBPs and to construct a prognostic model for clinical use. mRNA sequencing and clinical data for CRC were obtained from The Cancer Genome Atlas database (TCGA). Gene expression profiles were analyzed to identify differentially expressed RBPs using R and Perl software. Hub RBPs were filtered out using univariate Cox and multivariate Cox regression analysis. We used functional enrichment analysis, including Gene Ontology and Gene Set Enrichment Analysis, to perform the function and mechanisms of the identified RBPs. The nomogram predicted overall survival (OS). Calibration curves were used to evaluate the consistency between the predicted and actual survival rate, the consistency index (c-index) was calculated, and the prognostic effect of the model was evaluated. Finally, we identified 178 differently expressed RBPs, including 121 up-regulated and 57 down-regulated proteins. Our prognostic model was based on nine RBPs (PNLDC1, RRS1, HEXIM1, PPARGC1A, PPARGC1B, BRCA1, CELF4, AEN and NOVA1). Survival analysis showed that patients in the high-risk subgroup had a worse OS than those in the low-risk subgroup. The area under the curve value of the receiver operating characteristic curve of the prognostic model is 0.712 in the TCGA cohort and 0.638 in the GEO cohort. These results show that the model has a moderate diagnostic ability. The c-index of the nomogram is 0.77 in the TCGA cohort and 0.73 in the GEO cohort. We showed that the risk score is an independent prognostic biomarker and that some RBPs may be potential biomarkers for the diagnosis and prognosis of CRC.

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Integrated analysis of RNA-binding proteins in human colorectal cancer

Cited by 25 publications

References 79 publications

LINC01224 promotes colorectal cancer progression through targeting miR-485-5p/MYO6 axis

LINC01224 promotes colorectal cancer progression through targeting miR-485-5p/MYO6 axis

Identification of a Three-RNA Binding Proteins (RBPs) Signature Predicting Prognosis for Breast Cancer

Construction and validation of an RNA-binding protein-associated prognostic model for colorectal cancer

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