Analysis of the expression, function, prognosis and co-expression genes of DDX20 in gastric cancer

Wang, Qingshui; Yan, Ye; Lin, Rongbo; Weng, Shuyun; Cai, Fan; Mei, Zou; Niu, Haitao; Ge, Lilin; Lin, Yao

doi:10.1016/j.csbj.2020.09.002

Cited by 12 publications

(13 citation statements)

References 29 publications

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“…MicroRNAs (miRNA), which are short non-coding RNAs of ∼ 22 nucleotides, function by guiding AGO proteins to interact with complementary target RNAs, yielding the RNA-induced silencing complex (RISC) [4] , [5] . The formation of RISC can promote the translation repression of messenger RNA [6] , [7] or the degradation of exogenous pathogen RNA [8] . In addition to the key role in cellular process, microRNA has also been widely used as an experimental tool [9] , [10] and recent advances have gradually made miRNA therapeutics for clinical utility [11] , [12] , [13] , [14] .…”

Section: Introductionmentioning

confidence: 99%

Elucidation of the conformational dynamics and assembly of Argonaute–RNA complexes by distinct yet coordinated actions of the supplementary microRNA

Zhuang

Fan

et al. 2022

Computational and Structural Biotechnology Journal

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Section: Introductionmentioning

confidence: 99%

Elucidation of the conformational dynamics and assembly of Argonaute–RNA complexes by distinct yet coordinated actions of the supplementary microRNA

Zhuang

Fan

et al. 2022

Computational and Structural Biotechnology Journal

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“…The microarray dataset GSE66272, GSE36895, GSE46699, and GSE53757 were downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/), which were performed on Affymetrix Human Genome U133 Plus 2.0 Array platform. The method for extracting microarray gene expression values is based on our previous research (11). Then, we used ComBat for batch effect removal to homogenize the gene expression data from GSE66272, GSE36895, GSE46699, and GSE53757.…”

Section: Gene Expression Extractionmentioning

confidence: 99%

MCM2-7 in Clear Cell Renal Cell Carcinoma: MCM7 Promotes Tumor Cell Proliferation

Zhang¹,

Zhang²,

Wang³

et al. 2021

Front. Oncol.

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BackgroundClear cell renal cell carcinoma (ccRCC) accounts for 60-70% of renal cell carcinoma (RCC) cases. Finding more therapeutic targets for advanced ccRCC is an urgent mission. The minichromosome maintenance proteins 2-7 (MCM2-7) protein forms a stable heterohexamer and plays an important role in DNA replication in eukaryotic cells. In the study, we provide a comprehensive study of MCM2-7 genes expression and their potential roles in ccRCC.MethodsThe expression and prognosis of the MCM2-7 genes in ccRCC were analyzed using data from TCGA, GEO and ArrayExpress. MCM2-7 related genes were identified by weighted co-expression network analysis (WGCNA) and Metascape. CancerSEA and GSEA were used to analyze the function of MCM2–7 genes in ccRCC. The gene effect scores (CERES) of MCM2-7, which reflects carcinogenic or tumor suppressor, were obtained from DepMap. We used clinical and expression data of MCM2-7 from the TCGA dataset and the LASSO Cox regression analysis to develop a risk score to predict survival of patients with ccRCC. The correlations between risk score and other clinical indicators such as gender, age and stage were also analyzed. Further validation of this risk score was engaged in another cohort, E-MTAB-1980 from the ArrayExpress dataset.ResultsThe mRNA and protein expression of MCM2-7 were increased in ccRCC compared with normal tissues. High MCM2, MCM4, MCM6 and MCM7 expression were associated with a poor prognosis of ccRCC patients. Functional enrichment analysis revealed that MCM2-7 might influence the progress of ccRCC by regulating the cell cycle. Knockdown of MCM7 can inhibit the proliferation of ccRCC cells. A two-gene risk score including MCM4 and MCM6 can predict overall survival (OS) of ccRCC patients. The risk score was successfully verified by further using Arrayexpress cohort.ConclusionWe analyze MCM2-7 mRNA and protein levels in ccRCC. MCM7 is determined to promote tumor proliferation. Meanwhile, our study has determined a risk score model composed of MCM2-7 can predict the prognosis of ccRCC patients, which may help future treatment strategies.

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“…Four microarray gene expression datasets of TNBC patients (GSE31448, GSE45827, GSE53752, and GSE65216) were obtained from the GEO database. The method for extracting microarray gene expression values was based on our previous research (18)(19)(20).…”

Section: Extraction Of Gene Expression Data From Tnbc Patient Datasetsmentioning

confidence: 99%

An immunohistochemical panel of three small ubiquitin-like modifier genes predicts outcomes of patients with triple-negative breast cancer

et al. 2021

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Background: Triple-negative breast cancer (TNBC) is a highly heterogeneous and aggressive disease.Developing new candidate biomarkers for chemotherapy response and possible therapeutic targets has become an urgent clinical need. Small ubiquitin-like modifiers (SUMOs) mediate post-translational modifications (SUMOylation) has been shown to be involved in numerous biological processes. However, the role of SUMOylation in TNBC has yet to be elucidated. Method:The mRNA expression of SUMO1/2/3 was analyzed by the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus database (GEO) databases (N=412). We also evaluated the SUMO1/2/3 protein expression in 212 TNBC patients using immunohistochemical (IHC) staining method. A classifier with Least absolute shrinkage and selection operator (LASSO) Cox regression model was then built based on the associations between the expression of SUMO1/2/3 proteins and the disease-free survival (DFS) of TNBC patients.Results: Elevated SUMO1/2/3 levels were indicated to be associated with a poorer overall survival (OS) and DFS for TNBC patients. With the LASSO model, we built a classifier based on the IHC scores of SUMO1/2/3 proteins and named it the 'SB classifier'. Patients with SB classifier-defined high score were found to have an unfavorable response to chemotherapy [hazard ratio (HR) 4.04, 95% confidence interval (CI): 2.14-7.63; P<0.0001]. A nomogram was then developed to identify which patients might benefit from chemotherapy. Finally, our results also suggested that the activation of SUMOylation pathway in TNBC might be induced by MYC signaling. Conclusions:We constructed a reliable prognostic and predictive tool for TNBC patients treated with chemotherapy, which could facilitate individualized counseling and management. 1068 Lin et al. A prognosis panel for triple-negative breast cancer

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Analysis of the expression, function, prognosis and co-expression genes of DDX20 in gastric cancer

Abstract: Graphical abstract

Cited by 12 publications

References 29 publications

Elucidation of the conformational dynamics and assembly of Argonaute–RNA complexes by distinct yet coordinated actions of the supplementary microRNA

Elucidation of the conformational dynamics and assembly of Argonaute–RNA complexes by distinct yet coordinated actions of the supplementary microRNA

MCM2-7 in Clear Cell Renal Cell Carcinoma: MCM7 Promotes Tumor Cell Proliferation

An immunohistochemical panel of three small ubiquitin-like modifier genes predicts outcomes of patients with triple-negative breast cancer

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