Effects of RNA Binding Proteins on the Prognosis and Malignant Progression in Prostate Cancer

Hua, Xiaoliang; Ge, Shengdong; Chen, Juan; Zhang, Li; Tai, Sheng; Liang, Chaozhao

doi:10.3389/fgene.2020.591667

Cited by 16 publications

(14 citation statements)

References 51 publications

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“…SDF2L1 is an independent prognostic indicator in breast cancer, and the reduced level of SDF2L1 is related to poor clinical outcomes ( Jiang et al, 2009 ). Two signatures of RNA-binding proteins enrolled the CTU1 gene as a vital indicator to predict the survival of prostate cancer and bladder urothelial carcinoma ( Guo et al, 2020 ; Hua et al, 2020 ). However, the effects of these 10 genes in NBL have not been explored.…”

Section: Discussionmentioning

confidence: 99%

Development and Validation of a Five-RNA–Based Signature and Identification of Candidate Drugs for Neuroblastoma

Zhang

et al. 2021

Front. Genet.

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Neuroblastoma (NBL) originating from the sympathetic nervous system is the most prevalent solid tumor in infancy. Although there is sufficient variability in prognosis among different age pyramids, age-related gene expression profiles and biomarkers remain poorly explored. The present study aimed to construct a signature based on differentially expressed genes (DEGs) between two age groups in NBL. Univariate Cox regression, multivariate Cox regression, and LASSO analyses were used to identify the optimal prognostic factors. The prediction ability of the model was assessed using the receiver operating characteristic (ROC) curve and C-index. Functional enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes and gene ontology databases. A total of 1,160 DEGs were identified between the two groups, and 204 DEGs impacted the survival of NBL. Functional enrichment analysis revealed that the DEGs were involved in retinol metabolism, cholesterol metabolism, and glycolysis/gluconeogenesis pathways. Five RNAs, namely F8A3, PDF, ANKRD24, FAXDC2, and TMEM160 were recruited into the signature. They were correlated with COG risk classification, INSS stage, and histology. MYCN amplification was linked to FAXDC2, TMEM160, PDF, and F8A3. The expression levels of ANKRD24, PDF, and TMEM160 were lower in the hyperdiploid groups. Only FAXDC2 levels were different in the different MKI grades. The ROC curve showed that the five-RNA–based signatures effectively predicted the OS of NBL (3-years AUC = 0.791, 5-years AUC = 0.816) in the TARGET cohort. The predictive capability was also validated by the GSE49711 cohort (3-years AUC = 0.851, 5-years AUC = 0.848). The C-index in the TARGET and GSE49711 cohorts was 0.749 and 0.809, respectively. The potential mechanisms of the five RNAs were also explored via gene set enrichment analysis, and candidate drugs targeting the five genes, including dabrafenib, vemurafenib, and bafetinib, were screened. In conclusion, we constructed a five-RNA–based signature to predict the survival of NBL and screened candidate agents against NBL.

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Section: Discussionmentioning

confidence: 99%

Development and Validation of a Five-RNA–Based Signature and Identification of Candidate Drugs for Neuroblastoma

Zhang

et al. 2021

Front. Genet.

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“…Ming Zhang et al identi ed the copy number ampli cations of CTU1 in 25% of myxopapillary ependymomas by means of whole exome sequencing [43]. CTU1 has been identi ed as one of prognostic predictors for prostate cancer and bladder cancer [44,45]. We also identi ed NUFIP1 as a risk factor of CC patients.…”

Section: Discussionmentioning

confidence: 85%

Expression Profile of RNA Binding Protein in Cervical Cancer

Huang¹,

Li²,

Li³

2021

Preprint

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Background: It has been demonstrated by studies globally that RNA binding proteins (RBPs) took part in the development of cervical cancer (CC). Few studies concentrated on the correlation between RBPs and overall survival of CC patients. We retrieved significant DEGs (differently expressed genes, RNA binding proteins) correlated to the process of cervical cancer development. Methods: Expressions level of genes in cervical cancer and normal tissue samples were obtained from GTEx and TCGA database. Differently expressed RNA binding proteins (DEGs) were retrieved by Wilcoxon sum-rank test. ClusterProfiler package worked in R software was used to perform GO and KEGG enrichment analyses. Univariate propotional hazard cox regression and multivariate propotional hazard cox regressions were applied to identify DEGs equipped with prognostic value and other clinical independent risk factors. ROC curve was drawn for comparing the survival predict feasibility of risk score with other risk factors in CC patients. Nomogram was drawn to exhibit the prediction model and validated by C-index and calibration curve. Correlations between Differentially expressed RNA binding proteins (DEGs) and other clinical features were investigated by t test or Cruskal wallis analysis. Correlation between Immune and DEGs in cervical cancer was investigated by ssGSEA. Results: 347 differentially expressed RBPs (DEGs) were retrieved from cervical cancer tissue and normal tissue samples. GO enrichment analysis showed that these DEGs involved in RNA splicing, catabolic process and metabolism. Cox regression medel showed that there were ten DEGs significantly associated with overall survival of cervical caner patients. WDR43 (HR = 0.423, P=0.008), RBM38 (HR = 0.533, P<0.001), RNASEH2A (HR=0.474, P=0.002) and HENMT1 (HR=0.720, P=0.071) played protective roles in survival among these ten genes. Stage (Stage IV vs Stage I HR = 3.434, P<0.001) and risk score (HR = 1.214, P< 0.001) were sorted as independent prognostic risk factors based on multivariate cox regression. ROC curve validated that risk score was preferable to predict survival of CC patients than other risk factors. Additionally, we found some of these ten predictor DEGs were correlated significantly in statistic with tumor grade or stage, clinical T stage, clinical N stage, pathology or risk score (all P< 0.05). Part of immune cells and immune functions showed a lower activity in high risk group than low risk group which is distincted by median risk score. Conclusion: Our discovery showed that many RNA binding proteins involved in the progress of cervical cancer, which could probably serve as prognostic biomarkers and accelerate the discovery of treatment targets for CC patients.

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“…REXO2 is a RNA binding protein and is required for maintaining the integrity of mitochondria 44 , 45 . Previous reports showed that higher expression levels of REXO2 were associated with the poor prognosis of prostate cancer 46 . However, the expression and prognosis of REXO2 in other malignant disease, particular in glioma were unknown.…”

Section: Discussionmentioning

confidence: 90%

RUNX1 and REXO2 are associated with the heterogeneity and prognosis of IDH wild type lower grade glioma

Wang

et al. 2021

Sci Rep

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Based on isocitrate dehydrogenase (IDH) alterations, lower grade glioma (LGG) is divided into IDH mutant and wild type subgroups. However, the further classification of IDH wild type LGG was unclear. Here, IDH wild type LGG patients in The Cancer Genome Atlas and Chinese Glioma Genome Atlas were divided into two sub-clusters using non-negative matrix factorization. IDH wild type LGG patients in sub-cluster2 had prolonged overall survival and low frequency of CDKN2A alterations and low immune infiltrations. Differentially expressed genes in sub-cluster1 were positively correlated with RUNX1 transcription factor. Moreover, IDH wild type LGG patients with higher stromal score or immune score were positively correlated with RUNX1 transcription factor. RUNX1 and its target gene REXO2 were up-regulated in sub-cluster1 and associated with the worse prognosis of IDH wild type LGG. RUNX1 and REXO2 were associated with the higher immune infiltrations. Furthermore, RUNX1 and REXO2 were correlated with the worse prognosis of LGG or glioma. IDH wild type LGG in sub-cluster2 was hyper-methylated. REXO2 hyper-methylation was associated with the favorable prognosis of LGG or glioma. At last, we showed that, age, tumor grade and REXO2 expression were independent prognostic factors in IDH wild type LGG.

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Effects of RNA Binding Proteins on the Prognosis and Malignant Progression in Prostate Cancer

Cited by 16 publications

References 51 publications

Development and Validation of a Five-RNA–Based Signature and Identification of Candidate Drugs for Neuroblastoma

Development and Validation of a Five-RNA–Based Signature and Identification of Candidate Drugs for Neuroblastoma

Expression Profile of RNA Binding Protein in Cervical Cancer

RUNX1 and REXO2 are associated with the heterogeneity and prognosis of IDH wild type lower grade glioma

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