Identification of key DNA methylation-driven genes in prostate adenocarcinoma: an integrative analysis of TCGA methylation data

Xu, Ning; Wu, Yupeng; Ke, Zhi‐Bin; Liang, Yingchun; Cai, Hai; Su, Wenting; Tao, Xuan; Chen, Shao‐Hao; Zheng, Qing‐Shui; Wei, Yong; Xue, Xue-Yi

doi:10.1186/s12967-019-2065-2

Cited by 59 publications

(56 citation statements)

References 42 publications

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“…The Spearman's correlation analysis showed that the correlation of the certified target genes with miR-221-3p in HNSCC (Figure 13). [35]. In addition, a large number of valuable epidemiological studies have shown that UGT1A7 affects individuals' susceptibility to various cancers, such as pancreatic cancer [36],gastrointestinal carcinomas [37].Now our study suggests that miR-221- [38,39,40,41,42], a control the progression of the tumors.…”

Section: The Prospective Target Genes Of Mir-221 In Hnsccmentioning

confidence: 51%

Bioinformatics analysis of the expression and role of microRNA-221-3p in the head and neck squamous cell carcinoma

Zhou

Ji-xi

et al. 2020

Preprint

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Background Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer subtype globally, associated with a high rate of morbidity and mortality. However, the target genes of miR-221-3p and the underlying mechanism involved in HNSCC were not known. Therefore, in the current study, we studied the role of miR-221-3p in the HNSCC. Methods Tissues collected from 48 control and 21 HNSCC patients were processed to check the differential expression of miR-221-3p by Real-time RT-Polymerase Chain Reaction (RT-qPCR). Overexpression of microRNA-221-3p (miR-221-3p) is significantly correlated to the onset and progression of HNSCC. We also conducted the meta-analysis of the cancer literature from the cancer genome atlas (TCGA) and the Gene Expression Omnibus (GEO) database to estimate the expression of miR-221-3p in HNSCC. The miR-221-3p target genes in the HNSCC were predicted with the miRWalk and TCGA databases, and functionally annotated via the Gene Ontology Finally, Spearman’s analysis was used to determine the role of the related target genes in important pathways involved in the development of HNSCC. Results We observed a significantly higher expression of miR-221-3p in HNSCC compared to the normal with a summary receiver operating characteristic (sROC) of 0.86(95% Cl: 0.83,0.89). The KEGG and GO comprehensive analysis predicted that miR-221-3p might be involved in the development of HNSCC through the following metabolic pathways, viz Drug metabolism - cytochrome P450 UGT1A7 and MAOB may be important genes for the role of mir-221-3p. Conclusions Our results indicate that miR-221-3p may be used as a non-invasive and hypersensitive biomarker in the diagnosis. Thus, it can be concluded that miR-221-3p is an extremely important gene locus involved in the process of the deterioration and eventual tumorigenesis of HNSCC.

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Section: The Prospective Target Genes Of Mir-221 In Hnsccmentioning

confidence: 51%

Bioinformatics analysis of the expression and role of microRNA-221-3p in the head and neck squamous cell carcinoma

Zhou

Ji-xi

et al. 2020

Preprint

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“…And Wang et al elucidated that JAK/STAT3-dependent fatty acid beta-oxidation is associated with breast cancer chemoresistance [ 26 ]. Xu et al revealed that DNA methylation-driven genes in prostate adenocarcinoma were active in electron carrier activity [ 27 ]. What is more, KEGG pathway enrichment analysis uncovered that CPT2 and ACADL were both enriched in fatty acid degradation, fatty acid metabolism, and PPAR signaling pathway, which were all directly or indirectly involved in the process of lipid metabolism related to the progression of malignant tumors [ 28 – 31 ].…”

Section: Discussionmentioning

confidence: 99%

A Prognostic Model Based on Six Metabolism-Related Genes in Colorectal Cancer

Sun

Zhang

Guo

et al. 2020

BioMed Research International

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An increasing number of studies have shown that abnormal metabolism processes are closely correlated with the genesis and progression of colorectal cancer (CRC). In this study, we systematically explored the prognostic value of metabolism-related genes (MRGs) for CRC patients. A total of 289 differentially expressed MRGs were screened based on The Cancer Genome Atlas (TCGA) and the Molecular Signatures Database (MSigDB), and 72 differentially expressed transcription factors (TFs) were obtained from TCGA and the Cistrome Project database. The clinical samples obtained from TCGA were randomly divided at a ratio of 7 : 3 to obtain the training group (n=306) and the test group (n=128). After univariate and multivariate Cox regression analyses, we constructed a prognostic model based on 6 MRGs (AOC2, ENPP2, ADA, GPD1L, ACADL, and CPT2). Kaplan–Meier survival analysis of the training group, validation group, and overall samples proved that the model had statistical significance in predicting the outcomes of patients. Independent prognosis analysis suggested that this risk score might serve as an independent prognosis factor for CRC patients. Moreover, we combined the prognostic model and the clinical characteristics in a nomogram to predict the overall survival of CRC patients. Furthermore, gene set enrichment analysis (GSEA) was conducted to identify the enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in the high- and low-risk groups, which might provide novel therapeutic targets for CRC patients. We discovered through the protein-protein interaction (PPI) network and TF-MRG regulatory network that 7 hub genes were retrieved from the PPI network and 4 kinds of differentially expressed TFs (NR3C1, MYH11, MAF, and CBX7) positively regulated 4 prognosis-associated MRGs (GSTM5, PTGIS, ENPP2, and P4HA3).

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“…Such gene was identified as methylation-driven gene. Cancer-specific methylation-driven genes were demonstrated with vital clinical value [ 33 ].…”

Section: Discussionmentioning

confidence: 99%

Analysis of DNA methylation-driven genes for predicting the prognosis of patients with colorectal cancer

Fu¹,

Cheng²,

Wu³

et al. 2020

aging

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Identification of key DNA methylation-driven genes in prostate adenocarcinoma: an integrative analysis of TCGA methylation data

Cited by 59 publications

References 42 publications

Bioinformatics analysis of the expression and role of microRNA-221-3p in the head and neck squamous cell carcinoma

Bioinformatics analysis of the expression and role of microRNA-221-3p in the head and neck squamous cell carcinoma

A Prognostic Model Based on Six Metabolism-Related Genes in Colorectal Cancer

Analysis of DNA methylation-driven genes for predicting the prognosis of patients with colorectal cancer

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