Identification of biomarkers associated with diagnosis and prognosis of gastroesophageal junction adenocarcinoma–a study based on integrated bioinformatics analysis in GEO and TCGA database

Song, Danlei; Jian-guo, Tian; Hu, Yuping; Wei, Yongjian; Lü, Hong; Wang, Yuping; Guan, Qun; Zhou, Yongning

doi:10.1097/md.0000000000023605

Cited by 8 publications

(4 citation statements)

References 35 publications

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“…Also, there is a controversy on the prognostic role of HER2 status in ACGEJ patients ( 6 , 9 ). Genetic factors including microRNAs and genes are biomarkers associated with the diagnosis or prognosis of ACGEJ ( 10 , 11 ). The discovery of new biomarkers plays an important role in an early, rapid, and accurate determination of disease occurrence and prognosis of human cancers.…”

Section: Introductionmentioning

confidence: 99%

Expression and Prognostic Value of RAD51 in Adenocarcinoma at the Gastroesophageal Junction

Redati¹,

Yang²,

Liu³

et al. 2022

ijph

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Background: The RAD51 recombinase is involved in homologous recombination and DNA repair. However, the association of RAD51 with the prognosis of adenocarcinoma at the gastroesophageal junction (ACGEJ) is not clear. We aimed to investigate the association of RAD51with ACGEJ prognosis. Methods: The difference in the expression level of RAD51 between ACGEJ tumors and control tissues in the microarray datasets (GSE159721, GSE74553, and GSE96669) were compared. The online Kaplan-Meier plotter survival analysis and meta-analysis were used to analyze the association of RAD51 with overall survival in pan-cancers. MiRNAs targeting RAD51 were identified and their expression profiles in ACGEJ tumors were analyzed. Functional enrichment analysis was performed for miRNAs of RAD51. Results: RAD51 was upregulated in ACGEJ tumors compared with control tissues (P < 0.05). High RAD51 level was correlated with a poor prognosis in stomach adenocarcinoma and esophageal cancer. The meta-analysis showed that high RAD51 level was correlated with a poor prognosis in TCGA pan-cancers (P = 0.03). Six regulatory miRNAs of RAD51, including hsa-miR-182, hsa-miR-221, and hsa-miR-34a, were downregulated in ACGEJ tumor tissues and were associated with pathways including “fatty acid biosynthesis” and “viral carcinogenesis”. Conclusions: RAD51 is a potent prognostic biomarker in ACGEJ. MiRNAs including hsa-miR-182, hsa-miR-221, and hsa-miR-34a might play crucial roles in ACGEJ by regulating the RAD51 gene.

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Section: Introductionmentioning

confidence: 99%

Expression and Prognostic Value of RAD51 in Adenocarcinoma at the Gastroesophageal Junction

Redati¹,

Yang²,

Liu³

et al. 2022

ijph

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“…It is performed by detecting tens of thousands of gene expression information using a high-throughput pattern 23 . The GEO database is the most comprehensive public functional genomics database that includes gene expression, mutation, modification, and other related information 24 . Currently, the GEO database has 65,775 microarray expression profiling by array that has been queried and downloaded by users for free.…”

Section: Discussionmentioning

confidence: 99%

Identification of hub genes and candidate herbal treatment in obesity through integrated bioinformatic analysis and reverse network pharmacology

Tai

Yang²,

Feng³

et al. 2022

Sci Rep

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Obesity is a global epidemic elevating the risk of various metabolic disorders. As there is a lack of effective drugs to treat obesity, we combined bioinformatics and reverse network pharmacology in this study to identify effective herbs to treat obesity. We identified 1011 differentially expressed genes (DEGs) of adipose tissue after weight loss by analyzing five expression profiles (GSE103766, GSE35411, GSE112307, GSE43471, and GSE35710) from the Gene Expression Omnibus (GEO) database. We identified 27 hub genes from the protein–protein interaction (PPI) network by performing MCODE using the Search Tool for the Retrieval of Interacting Genes (STRING) database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that these hub genes have roles in the extracellular matrix–receptor interaction, cholesterol metabolism, PI3K-Akt signaling pathway, etc. Ten herbs (Aloe, Portulacae Herba, Mori Follum, Silybum Marianum, Phyllanthi Fructus, Pollen Typhae, Ginkgo Semen, Leonuri Herba, Eriobotryae Folium, and Litseae Fructus) targeting the nine hub genes (COL1A1, MMP2, MMP9, SPP1, DNMT3B, MMP7, CETP, COL1A2, and MUC1) using six ingredients were identified as the key herbs. Quercetin and (-)-epigallocatechin-3-gallate were determined to be the key ingredients. Lastly, Ingredients-Targets, Herbs-Ingredients-Targets, and Herbs-Taste-Meridian Tropism networks were constructed using Cytoscape to elucidate this complex relationship. This study could help identify promising therapeutic targets and drugs to treat obesity.

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“…The PPI network (confidence score > 0.7), with KEGG annotations, was visualized using Cytoscape ( Shannon et al, 2003 ). The hub genes were identified using the Cytoscape plugin CytoHubba ( Song et al, 2020 ; Zuo et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Unraveling the Genetic Basis of Fertility Restoration for Cytoplasmic Male Sterile Line WNJ01A Originated From Brassica juncea in Brassica napus

Yang

Nong

et al. 2021

Front. Plant Sci.

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Crosses that lead to heterosis have been widely used in the rapeseed (Brassica napus L.) industry. Cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) systems represent one of the most useful tools for rapeseed production. Several CMS types and their restorer lines have been identified in rapeseed, but there are few studies on the mechanisms underlying fertility restoration. Here, we performed morphological observation, map-based cloning, and transcriptomic analysis of the F2 population developed by crossing the CMS line WNJ01A with its restorer line Hui01. Paraffin-embedded sections showed that the sporogenous cell stage was the critical pollen degeneration period, with major sporogenous cells displaying loose and irregular arrangement in sterile anthers. Most mitochondrial electron transport chain (mtETC) complex genes were upregulated in fertile compared to sterile buds. Using bulked segregant analysis (BSA)-seq to analyze mixed DNA pools from sterile and fertile F2 buds, respectively, we identified a 6.25 Mb candidate interval where Rfw is located. Using map-based cloning experiments combined with bacterial artificial chromosome (BAC) clone sequencing, the candidate interval was reduced to 99.75 kb and two pentatricopeptide repeat (PPR) genes were found among 28 predicted genes in this interval. Transcriptome sequencing showed that there were 1679 DEGs (1023 upregulated and 656 downregulated) in fertile compared to sterile F2 buds. The upregulated differentially expressed genes (DEGs) were enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) lysine degradation pathway and phenylalanine metabolism, and the downregulated DEGs were enriched in cutin, suberine, and wax biosynthesis. Furthermore, 44 DEGs were involved in pollen and anther development, such as tapetum, microspores, and pollen wall development. All of them were upregulated except a few such as POE1 genes (which encode Pollen Ole e I allergen and extensin family proteins). There were 261 specifically expressed DEGs (9 and 252 in sterile and fertile buds, respectively). Regarding the fertile bud-specific upregulated DEGs, the ubiquitin–proteasome pathway was enriched. The top four hub genes in the protein–protein interaction network (BnaA09g56400D, BnaA10g18210D, BnaA10g18220D, and BnaC09g41740D) encode RAD23d proteins, which deliver ubiquitinated substrates to the 26S proteasome. These findings provide evidence on the pathways regulated by Rfw and improve our understanding of fertility restoration.

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Identification of biomarkers associated with diagnosis and prognosis of gastroesophageal junction adenocarcinoma–a study based on integrated bioinformatics analysis in GEO and TCGA database

Cited by 8 publications

References 35 publications

Expression and Prognostic Value of RAD51 in Adenocarcinoma at the Gastroesophageal Junction

Expression and Prognostic Value of RAD51 in Adenocarcinoma at the Gastroesophageal Junction

Identification of hub genes and candidate herbal treatment in obesity through integrated bioinformatic analysis and reverse network pharmacology

Unraveling the Genetic Basis of Fertility Restoration for Cytoplasmic Male Sterile Line WNJ01A Originated From Brassica juncea in Brassica napus

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