scholarly journals Development and Validation of a Novel Five-Gene-Based RNA Binding Protein Associated Prognostic Model for Human Colon Cancer

2020 ◽  
Author(s):  
Haoling Liu ◽  
Qingquan Bai ◽  
Zhaoyang Lu ◽  
Xuan Song ◽  
Yao Liu ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Prognostic Model ◽  
Rna Binding ◽  
Malignant Tumors ◽  
Binding Protein ◽  
Characteristic Curve ◽  
Rna Binding Protein ◽  
The Cancer Genome Atlas ◽  
Human Colon Cancer ◽  
Good Ability

Abstract Background: Dysregulation of RNA binding protein (RBP) expression has been reported in various malignant tumors, and it is related to the occurrence and development of cancer. However, the role of RBPs in colon cancer remains unclear. Methods: We downloaded the RNA sequencing data of colon cancer from The Cancer Genome Atlas (TCGA) database, and determined the differently expressed RBPs between normal and cancer tissues. Then, through a series of bioinformatics analysis, we systematically studied the expression and prognostic value of these RBPs.Result: A total of 490 different expression differently expressed RBPs were identified, including 323 up-regulated and 167 down regulated RBPs. Five RBPs (PNLDC1, NSUN6, NOL3, PPARGC1A, LRRFIP2) were identified as prognosis related genes for the construction of prognostic model. Further analysis showed that the overall survival rate (OS) of patients in the high-risk subgroup was worse than that in the low-risk subgroup based on this model. The area under the characteristic curve of time-dependent receiver was 0.691 in TCGA and 0.624 in GEO, which confirmed the prognostic model to be a good one. We also established a nominal map based on the internal validation in 5 RBPs mRNAs and TCGA sequeues, showing a good ability to differentiate colon cancer.Conclusions: We screened RBPs expression differences between colon cancer and adjacent non tumor colon tissues using the TCGA database to identify potential gene biomarkers.Besides,a very effective prediction model was constructed and tested based on the differential expression of RBPs using the TCGA and Gene Expression Omnibus (GEO) database.We also Validated of the relationship between the expression of five RBPs and prognosis

scholarly journals Development and validation of a novel five-gene-based RNA binding protein associated prognostic model for human colon cancer

2020 ◽  
Author(s):  
Haoling Liu ◽  
Qingquan Bai ◽  
Zhaoyang Lu ◽  
Xuan Song ◽  
Ye Jin ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Prognostic Model ◽  
Rna Binding ◽  
Malignant Tumors ◽  
Binding Protein ◽  
Characteristic Curve ◽  
Rna Binding Protein ◽  
The Cancer Genome Atlas ◽  
Human Colon Cancer ◽  
Good Ability

Abstract BackgroundDysregulation of RNA binding protein (RBP) expression has been reported in various malignant tumors, and it is related to the occurrence and development of cancer. However, the role of RBPs in colon cancer remains unclear.MethodsWe downloaded the RNA sequencing data of colon cancer from The Cancer Genome Atlas (TCGA) database, and determined the differently expressed RBPs between normal and cancer tissues. Then, through a series of bioinformatics analysis, we systematically studied the expression and prognostic value of these RBPs.ResultA total of 490 different expression differently expressed RBPs were identified, including 323 up-regulated and 167 down. regulated RBPs. Five RBPs (PNLDC1, NSUN6, NOL3, PPARGC1A, LRRFIP2) were identified as prognosis related genes for the construction of prognostic model. Further analysis showed that the overall survival rate (OS) of patients in the high-risk subgroup was worse than that in the low-risk subgroup based on this model. The area under the characteristic curve of time-dependent receiver was 0.691 in TCGA and 0.624 in GEO, which confirmed the prognostic model to be a good one. We also established a nominal map based on the internal validation in 5 RBPs mRNAs and TCGA sequeues, showing a good ability to differentiate colon cancer.ConclusionsWe screened RBPs expression differences between colon cancer and adjacent non tumor colon tissues using the TCGA database to identify potential gene biomarkers.Besides,a very effective prediction model was constructed and tested based on the differential expression of RBPs using the TCGA and Gene Expression Omnibus (GEO) database.We also Validated of the relationship between the expression of five RBPs and prognosis

scholarly journals Identification and Validation of RNA Binding Protein-associated Prognostic Model for Neuroblastoma

2020 ◽  
Author(s):  
JUN YANG ◽  
Jiaying Zhou ◽  
Cuili Li ◽  
Shaohua Wang
Keyword(s):  
Survival Rate ◽  
Prognostic Model ◽  
Rna Binding ◽  
Binding Protein ◽  
Characteristic Curve ◽  
Rna Binding Protein ◽  
Receiver Operator Characteristic Curve ◽  
Validation Data ◽  
Data Set ◽  
Significant Difference

Abstract Background: The abnormal expression of RNA binding protein (RBP) may be related to the development and progress of cancer. However, little is known about the mechanism of RBP in neuroblastoma (NB). Methods: We downloaded the RNA expression data of NB and normal nervous tissues from the (TARGET) database and GTEx database, and determined the differential expression of RBP between normal and cancerous tissues. Then the function and prognostic value of these RBPs were systematically studied. Results: A total of 348 differentially expressed RBPs were identified, together with 166 up-regulated RBPs and 182 down-regulated RBPs. Two hub RBPs (CPEB3 and CTU1) were identified as prognostic-related genes and chose to build prognostic risk score models. Further analysis showed that based on this model, the overall survival rate of patients in the high-risk subgroup was lower (P=2.152e-04). The area under the curve(AUC) of the receiver-operator characteristic curve(ROC) of the prognostic model is 0.720 in the TARGET cohort. There is a significant difference in the survival rate of patients in the high and low risk subgroups in the validation data set GSE85047 (P = 0.1237e-08), the AUC is 0.730. Conclusions: RNA binding protein (CPEB3 and CTU1) can be used as molecular markers of NB.

scholarly journals Identification and validation of RNA binding protein-associated prognostic model for Neuroblastoma

2021 ◽  
Author(s):  
Jun Yang ◽  
Jiaying Zhou ◽  
Cuili Li ◽  
Shaohua Wang
Keyword(s):  
Survival Rate ◽  
Prognostic Model ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Characteristic Curve ◽  
Rna Binding Protein ◽  
Validation Data ◽  
Data Set ◽  
Significant Difference

Abstract ABSTRACT Background: The abnormal expression of RNA binding protein (RBP) may be related to the development and progress of cancer. However, little is known about the mechanism of RBP in neuroblastoma (NB). Methods: We downloaded the RNA expression data of NB and normal nervous tissues from the (TARGET) database and GTEx database, and determined the differential expression of RBP between normal and cancerous tissues. Then the function and prognostic value of these RBPs were systematically studied. Results: A total of 348 differentially expressed RBPs were identified, together with 166 up-regulated RBPs and 182 down-regulated RBPs. Two hub RBPs (CPEB3 and CTU1) were identified as prognostic-related genes and chose to build prognostic risk score models. Further analysis showed that based on this model, the overall survival rate of patients in the high-risk subgroup was lower (P=2.152e-04). The area under the curve(AUC) of the receiver-operator characteristic curve(ROC) of the prognostic model is 0.720 in the TARGET cohort. There is a significant difference in the survival rate of patients in the high and low risk subgroups in the validation data set GSE85047 (P = 0.1237e-08), the AUC is 0.730. Conclusions: RNA binding protein (CPEB3 and CTU1) can be used as molecular markers of NB. Keywords: Neuroblastoma, RNA binding proteins, prognostic, TARGET, GTEx

scholarly journals Identification of RNA Binding Protein Signature to Predict Overall Survival for Bladder Cancer

2021 ◽  
Author(s):  
Danxia Li ◽  
Wenkai Han ◽  
Kai Che ◽  
haitao niu
Keyword(s):  
Overall Survival ◽  
Rna Binding ◽  
Risk Model ◽  
Rna Binding Proteins ◽  
Malignant Tumors ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Test Group ◽  
Enrichment Analysis ◽  
The Cancer Genome Atlas

Abstract Background: Bladder urothelial cancer (BLCA) is the 10th most common and 13th most deadly cancer globally. RNA binding proteins (RBPs) were reported to participate in the occurrence and progression of varieties of diseases, including malignant tumors. However, the role of RBPs in BLCA is rarely reported. Methods: We downloaded the transcriptome sequence gene expression data and the related clinical data from the cancer genome atlas (TCGA) database, and identified the differently expressed RBPs between BLCA and normal tissues. We explored the biological function by gene ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes database (KEGG) enrichment analysis. 388 key RBPs were obtained by protein-protein interaction (PPI). We constructed a prognostic risk model, explored the risk score related to BLCA, and validated the results both in the test group and HPA database. Results: In total, 388 differently expressed RBPs were discovered. Five prognostically relevant hub RBPs (YARS, EFTUD2, OAS1, DARS2, TRIM71) were used to construct a prognostic model based on multiple Cox analysis. We found that the overexpression of YARS, EFTUD2, DARS2, and TRIM71 were unfavorable prognostic factors for BLCA patients. Furthermore, we validated the results by the TCGA cohort and the Human Protein Atlas (HPA) database. Conclusion: We identified five RNA binding protein signatures to predict the overall survival for BLCA patients, which provide new insights for the pathogenesis and treatment of BLCA.

scholarly journals RNA-binding protein RALY reprogrammes mitochondrial metabolism via mediating miRNA processing in colorectal cancer

Gut ◽  
2020 ◽  
pp. gutjnl-2020-320652
Author(s):  
Lei Sun ◽  
Arabella Wan ◽  
Zhuolong Zhou ◽  
Dongshi Chen ◽  
Heng Liang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Rna Binding ◽  
Tumour Progression ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cancer Therapeutics ◽  
Mitochondrial Metabolism ◽  
The Cancer Genome Atlas ◽  
Colorectal Tumour ◽  
Specific Subset

ObjectiveDysregulated cellular metabolism is a distinct hallmark of human colorectal cancer (CRC). However, metabolic programme rewiring during tumour progression has yet to be fully understood.DesignWe analysed altered gene signatures during colorectal tumour progression, and used a complex of molecular and metabolic assays to study the regulation of metabolism in CRC cell lines, human patient-derived xenograft mouse models and tumour organoid models.ResultsWe identified a novel RNA-binding protein, RALY (also known as hnRNPCL2), that is highly associated with colorectal tumour aggressiveness. RALY acts as a key regulatory component in the Drosha complex, and promotes the post-transcriptional processing of a specific subset of miRNAs (miR-483, miR-676 and miR-877). These miRNAs systematically downregulate the expression of the metabolism-associated genes (ATP5I, ATP5G1, ATP5G3 and CYC1) and thereby reprogramme mitochondrial metabolism in the cancer cell. Analysis of The Cancer Genome Atlas (TCGA) reveals that increased levels of RALY are associated with poor prognosis in the patients with CRC expressing low levels of mitochondrion-associated genes. Mechanistically, induced processing of these miRNAs is facilitated by their N6-methyladenosine switch under reactive oxygen species (ROS) stress. Inhibition of the m6A methylation abolishes the RALY recognition of the terminal loop of the pri-miRNAs. Knockdown of RALY inhibits colorectal tumour growth and progression in vivo and in organoid models.ConclusionsCollectively, our results reveal a critical metabolism-centric role of RALY in tumour progression, which may lead to cancer therapeutics targeting RALY for treating CRC.

854 – Rna Binding Protein Imp1 Promotes Exosome Production in Colon Cancer

2019 ◽  
Vol 156 (6) ◽  
pp. S-188
Author(s):  
Sarah F. Andres ◽  
Ranjan Preet ◽  
Sukanya Das ◽  
Jiegang Yang ◽  
Priya Chatterji ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein

scholarly journals The RNA-Binding Protein Musashi1: A Major Player in Intestinal Epithelium Renewal and Colon Cancer Development

2012 ◽  
Vol 8 (4) ◽  
pp. 290-297 ◽  
Author(s):  
Michelina Plateroti ◽  
Patricia Rosa de Araujo ◽  
Acarizia Eduardo da Silva ◽  
Luiz O. F. Penalva
Keyword(s):  
Colon Cancer ◽  
Intestinal Epithelium ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cancer Development ◽  
Major Player
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