Expression of TDRD9 in a subset of lung carcinomas by CpG island hypomethylation protects from DNA damage

Guijo, Macarena; Ceballos-Chávez, María; Gómez-Marín, Elena; Basurto-Cayuela, Laura; Reyes, José Carlos Castañeda

doi:10.18632/oncotarget.22709

Cited by 21 publications

(12 citation statements)

References 50 publications

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“…TDRDs have now been detected in various cancers. TDRD9 is highly expressed in a subset of non-small cell lung carcinomas and derived cell lines through hypomethylation of its CpG island [ 16 ]. TDRD1 is closely associated with ERG overexpression in primary prostate cancer [ 17 ].…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis of RNA-binding proteins in human colorectal cancer

et al. 2020

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Background: Although RNA-binding proteins play an essential role in a variety of different tumours, there are still limited efforts made to systematically analyse the role of RNA-binding proteins (RBPs) in the survival of colorectal cancer (CRC) patients. Methods: Analysis of CRC transcriptome data collected from the TCGA database was conducted, and RBPs were extracted from CRC. R software was applied to analyse the differentially expressed genes (DEGs) of RBPs. To identify related pathways and perform functional annotation of RBP DEGs, Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out using the database for annotation, visualization and integrated discovery. Protein-protein interactions (PPIs) of these DEGs were analysed based on the Search Tool for the Retrieval of Interacting Genes (STRING) database and visualized by Cytoscape software. Based on the Cox regression analysis of the prognostic value of RBPs (from the PPI network) with survival time, the RBPs related to survival were identified, and a prognostic model was constructed. To verify the model, the data stored in the TCGA database were designated as the training set, while the chip data obtained from the GEO database were treated as the test set. Then, both survival analysis and ROC curve verification were conducted. Finally, the risk curves and nomograms of the two groups were generated to predict the survival period. Results: Among RBP DEGs, 314 genes were upregulated while 155 were downregulated, of which twelve RBPs (NOP14, MRPS23, MAK16, TDRD6, POP1, TDRD5, TDRD7, PPARGC1A, LIN28B, CELF4, LRRFIP2, MSI2) with prognostic value were obtained. Conclusions: The twelve identified genes may be promising predictors of CRC and play an essential role in the pathogenesis of CRC. However, further investigation of the underlying mechanism is needed.

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Section: Discussionmentioning

confidence: 99%

Integrated analysis of RNA-binding proteins in human colorectal cancer

et al. 2020

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“…TDRDs have now been detected in various cancers. TDRD9 is highly expressed in a subset of non-small cell lung carcinomas and derived cell lines by hypomethylation of its CpG island [16]. TDRD1 is closely associated with ERG over-expression in primary prostate cancer [17].…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis of RNA binding proteins in human colorectal cancer

Fan

Liu

Shi

et al. 2020

Preprint

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Background: Though RNA-binding proteins play an essential role in a variety of different tumors, there is still limited effort made on the systematic analysis of RNA binding proteins (RBPs) in the survival of colorectal cancer(CRC).Methods: An analysis was conducted of the CRC transcriptome data collected from the TCGA database and RBPs were extracted from CRC. R software was applied to analyze the differentially expressed genes (DEGs) of RBPs. To identify the pathways and functional annotation of RBPs DEGs, Gene Ontology (GO) function, Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis were carried out using the database for annotation, visualization and integrated discovery. The interactive gene database search tool was employed to conduct protein-protein interaction analysis, while Cytoscape software was applied for visual processing. Based on the COX regression analysis of the prognostic value of interacting RBPs and survival time, the RBPs related to survival were screened out, and a prognostic model was constructed. The data stored in TCGA database was taken as the Train group, while the chip data obtained from the GEO database was treated as the Test group to verify the model. Then, both survival analysis and ROC curve verification were conducted. Finally, the risk curves and nomograms of the two groups were drawn to predict the survival period.Results: There were 314 genes up-regulated by RBPs DEGs and 155 genes down-regulated, from which twelve RBPs (NOP14, MRPS23, MAK16, TDRD6, POP1, TDRD5, TDRD7, PPARGC1A, LIN28B, CELF4, LRRFIP2, MSI2) with prognostic markers were obtained.Conclusions: These twelve genes may be applicable as the predictor of CRC and play an essential role in the pathogenesis of CRC. In spite of this, it remains necessary to further explore the underlying mechanism.

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“…A subset of imprinted genes, including TDRD9, DPPA5, GFI1, MTTP, CDX1, WNT2, ITGA2, TCF7, MAML2 and WNT5A, possessed CpG islands in their promoter, which showed hypermethylation or hypomethylation of CpG islands from previous studies. The TDRD9 CpG island is hypomethylated and has a high expression level in non-small cell carcinomas, whereas hypermethylation will lead to nonexpression of TDRD9 [31]. The silencing of DPPA5 is associated with increased methylation in its CpG island promoter in differentiated embryonic carcinoma cells [32].…”

Section: Discussionmentioning

confidence: 99%

Identification of porcine imprinted genes involved in skeletal muscle development by high-throughput sequencing

Hou

Wang

et al. 2020

Preprint

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Background Imprinted genes—exhibiting parent-specific transcription—play essential roles in the process of mammalian development and growth. To further understand the imprinted genes involved in skeletal muscle development, DNA-seq and RNA-seq were used to explore the characteristics of imprinted genes involved in skeletal muscle development from porcine reciprocal crosses. Results A total of 211 paternally and 417 maternally imprinted genes were obtained in this study. Of the candidate imprinted genes, 50 paternally and 112 maternally imprinted genes possessed cytosine and guanine dinucleotide (CpG) islands in their promoters that may have regulated the imprinted gene expression. Imprint-related motifs were predicted and PBX1 motifs may mediate the expression of imprinted genes in the process of skeletal-muscle development. Functional analysis showed that a maternally imprinted gene of EPHB1 was involved in skeletal muscle cell proliferation. Imprinted genes involved in the biological processes of cell proliferation, differentiation and fusion were also analyzed. More maternally imprinted genes, including ADRA1D, E2F1, FBXO40, GHRH and WNT5A, were involved in skeletal muscle development than paternally imprinted genes. Conclusions Skeletal muscle development is crucial for meat production. This study identified 628 porcine imprinted genes in skeletal muscle and revealed their functional role in skeletal muscle development. Our findings should further assist with the potential use of imprinted genes in pig breeding.

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Expression of TDRD9 in a subset of lung carcinomas by CpG island hypomethylation protects from DNA damage

Cited by 21 publications

References 50 publications

Integrated analysis of RNA-binding proteins in human colorectal cancer

Integrated analysis of RNA-binding proteins in human colorectal cancer

Integrated analysis of RNA binding proteins in human colorectal cancer

Identification of porcine imprinted genes involved in skeletal muscle development by high-throughput sequencing

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