Identification of key pathways and genes in Barrett's esophagus using integrated bioinformatics methods

Zhang, Cong; Shen, Yujie; Wang, Jiazheng; Zhou, Mingxia; Chen, Yingwei

doi:10.3892/mmr.2017.8274

Cited by 3 publications

(2 citation statements)

References 45 publications

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“…As a common complication of GERD, the incidence of BE is rapidly increasing 3 . Therefore , it can be confirmed is that the overall prevalence of BE is increasing 5 . However, the molecular mechanism of BE is still unclear.…”

Section: Introductionmentioning

confidence: 83%

Analysis of immune related gene expression profiles and immune cell components in patients with Barrett esophagus

Shi

Guo

Chen

et al. 2022

Sci Rep

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Barrett's esophagus (BE) is a well-known precancerous condition of esophageal adenocarcinoma. However, the immune cells and immune related genes involved in BE development and progression are not fully understood. Therefore, our study attempted to investigate the roles of immune cells and immune related genes in BE patients. The raw gene expression data were downloaded from the GEO database. The limma package in R was used to screen differentially expressed genes (DEGs). Then we performed the least absolute shrinkage and selection operator (LASSO) and random forest (RF) analyses to screen key genes. The proportion of infiltrated immune cells was evaluated using the CIBERSORT algorithm between BE and normal esophagus (NE) samples. The spearman index was used to show the correlations of immune genes and immune cells. Receiver operating characteristic (ROC) curves were used to assess the diagnostic value of key genes in BE. A total of 103 differentially expressed immune-related genes were identified between BE samples and normal samples. Then, 7 genes (CD1A, LTF, FABP4, PGC, TCF7L2, INSR,SEMA3C) were obtained after Lasso analysis and RF modeling. CIBERSORT analysis revealed that resting CD4 T memory cells and gamma delta T cells were present at significantly lower levels in BE samples. Moreover, plasma cell and regulatory T cells were present at significantly higher levels in BE samples than in NE samples. INSR had the highest AUC values in ROC analysis. We identified 7 immune related genes and 4 different immune cells in our study, that may play vital roles in the occurrence and development of BE. Our findings improve the understanding of the molecular mechanisms of BE.

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Section: Introductionmentioning

confidence: 83%

Analysis of immune related gene expression profiles and immune cell components in patients with Barrett esophagus

Shi

Guo

Chen

et al. 2022

Sci Rep

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“…Furthermore, patients with CF have higher rates of delayed gastric emptying (up to 33%) and increased duodenogastro-esophageal reflux, which may contribute to more severe GERD[ 30 ]. Prolonged exposure of the esophageal mucosa to both stomach acid and bile acid may result in a premalignant lesion to EAC, known as Barrett’s esophagus (BE)[ 29 , 31 , 32 ]. Multiple studies have shown an increased risk for BE with CF[ 33 ], especially after liver transplantation[ 29 , 34 ].…”

Section: Rationale For Screening Of Gi and Hepatopancreatobiliary Cancersmentioning

confidence: 99%

Screening strategy for gastrointestinal and hepatopancreatobiliary cancers in cystic fibrosis

Hoskins

Wasuwanich

Scheimann

et al. 2021

WJGO

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Based on systematic review and meta-analysis, the risk for developing cancers in patients with cystic fibrosis (CF) is known to be significantly greater than in the general population, including site-specific cancers of the esophagus, small bowel, colon, liver, biliary tract, and pancreas. An even higher risk has been found in patients who have severe CF transmembrane conductance regulator ( CFTR ) genotypes or who have undergone organ transplantation and are immunosuppressed. The risk continues to rise as life expectancies steadily climb due to advancements in medical care and treatment for CF. The colorectal cancer risk is at such a high level that CF has now been declared a hereditary colon cancer syndrome by the Cystic Fibrosis Foundation. The CFTR gene has been strongly-associated with the development of gastrointestinal (GI) cancers and mortality in the CF population. Even CF carriers have shown an increased rate of GI cancers compared to the general population. Several limitations exist with the reported guidelines for screening of GI and hepatopancreatobiliary cancers in the CF population, which are largely universal and are still emerging. There is a need for more precise screening based on specific risk factors, including CFTR mutation, medical co-morbidities (such as gastroesophageal reflux disease, distal intestinal obstruction syndrome, and diabetes mellitus), familial risks for each cancer, gender, age, and other factors. In this review, we propose changes to the guidelines for GI screening of patients with CF. With the development of CFTR modulators, additional studies are necessary to elucidate if there is an effect on cancer risk.

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Identification of hub genes and key pathways in arsenic-treated rice (<i>Oryza sativa</i> L.) based on 9 topological analysis methods of CytoHubba

Yu,

Wang,

Dai

et al. 2024

Environ Health Prev Med

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Background: Arsenic is a toxic metalloid that can cause acute and chronic adverse health problems. Unfortunately, rice, the primary staple food for more than half of the world's population, is generally regarded as a typical arsenic-accumulating crop plant. Evidence indicates that arsenic stress can influence the growth and development of the rice plant, and lead to high concentrations of arsenic in rice grain. But the underlying mechanisms remain unclear. Methods: In the present research, the possible molecules and pathways involved in rice roots in response to arsenic stress were explored using bioinformatics methods. Datasets that involving arsenic-treated rice root and the "study type" that was restricted to "Expression profiling by array" were selected and downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between the arsenic-treated group and the control group were obtained using the online web tool GEO2R. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to investigate the functions of DEGs. The protein-protein interactions (PPI) network and the molecular complex detection algorithm (MCODE) of DEGs were analyzed using STRING and Cystoscope, respectively. Important nodes and hub genes in the PPI network were predicted and explored using the Cytoscape-cytoHubba plug-in. Results: Two datasets, GSE25206 and GSE71492, were downloaded from Gene Expression Omnibus (GEO) database. Eighty common DEGs from the two datasets, including sixty-three up-regulated and seventeen down-regulated genes, were then selected. After functional enrichment analysis, these common DEGs were enriched mainly in 10 GO items, including glutathione transferase activity, glutathione metabolic process, toxin catabolic process, and 7 KEGG pathways related to metabolism. After PPI network and MCODE analysis, 49 nodes from the DEGs PPI network were identified, filtering two significant modules. Next, the Cytoscape-cytoHubba plug-in was used to predict important nodes and hub genes. Finally, five genes [Os01g0644000, PRDX6 (Os07g0638400), PRX112 (Os07g0677300), ENO1(Os06g0136600), LOGL9 (Os09g0547500)] were verified and could serve as the best candidates associated with rice root in response to arsenic stress. Conclusions: In summary, we elucidated the potential pathways and genes in rice root in response to arsenic stress through a comprehensive bioinformatics analysis.

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Identification of key pathways and genes in Barrett's esophagus using integrated bioinformatics methods

Cited by 3 publications

References 45 publications

Analysis of immune related gene expression profiles and immune cell components in patients with Barrett esophagus

Analysis of immune related gene expression profiles and immune cell components in patients with Barrett esophagus

Screening strategy for gastrointestinal and hepatopancreatobiliary cancers in cystic fibrosis

Identification of hub genes and key pathways in arsenic-treated rice (<i>Oryza sativa</i> L.) based on 9 topological analysis methods of CytoHubba

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