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Gene expression profiling in gastric mucosa from Helicobacter pylori-infected and uninfected patients undergoing chronic superficial gastritis.

Yang ZM, Chen WW, Wang YF - PLoS ONE (2012)

Bottom Line: The annotated genes were involved in protein metabolism, inflammatory and immunological reaction, signal transduction, gene transcription, trace element metabolism, and so on.The 82% of these genes (28/34) were categorized in three molecular interaction networks involved in gene expression, cancer progress, antigen presentation and inflammatory response.The expression data of the array hybridization was confirmed by quantitative real-time PCR assays.

View Article: PubMed Central - PubMed

Affiliation: Pi-Wei Institute, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.

ABSTRACT
Helicobacter pylori infection reprograms host gene expression and influences various cellular processes, which have been investigated by cDNA microarray using in vitro culture cells and in vivo gastric biopsies from patients of the Chronic Abdominal Complaint. To further explore the effects of H. pylori infection on host gene expression, we have collected the gastric antral mucosa samples from 6 untreated patients with gastroscopic and pathologic confirmation of chronic superficial gastritis. Among them three patients were infected by H. pylori and the other three patients were not. These samples were analyzed by a microarray chip which contains 14,112 cloned cDNAs, and microarray data were analyzed via BRB ArrayTools software and Ingenuity Pathways Analysis (IPA) website. The results showed 34 genes of 38 differentially expressed genes regulated by H. pylori infection had been annotated. The annotated genes were involved in protein metabolism, inflammatory and immunological reaction, signal transduction, gene transcription, trace element metabolism, and so on. The 82% of these genes (28/34) were categorized in three molecular interaction networks involved in gene expression, cancer progress, antigen presentation and inflammatory response. The expression data of the array hybridization was confirmed by quantitative real-time PCR assays. Taken together, these data indicated that H. pylori infection could alter cellular gene expression processes, escape host defense mechanism, increase inflammatory and immune responses, activate NF-κB and Wnt/β-catenin signaling pathway, disturb metal ion homeostasis, and induce carcinogenesis. All of these might help to explain H. pylori pathogenic mechanism and the gastroduodenal pathogenesis induced by H. pylori infection.

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Related in: MedlinePlus

IPA network analysis of molecule interactions.The focus genes differentially expressed in this study were indicated by red symbols (up-regulated) and green symbols (down-regulated). The non-focus genes were not shown to be significant difference by the microarray analysis, and placed in the network by the Ingenuity software as intermediate molecules which were denoted by open symbols. Whereas symbols represented functional categories of the molecules are listed in the legend.
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pone-0033030-g003: IPA network analysis of molecule interactions.The focus genes differentially expressed in this study were indicated by red symbols (up-regulated) and green symbols (down-regulated). The non-focus genes were not shown to be significant difference by the microarray analysis, and placed in the network by the Ingenuity software as intermediate molecules which were denoted by open symbols. Whereas symbols represented functional categories of the molecules are listed in the legend.

Mentions: To interpret differentially expressed genes of H. pylori infection in the context of biological processes, pathways and networks, IPA Core Analyses were conducted and three high scoring networks (score>15) including 82% (28/34) of differentially expressed genes were identified (Figure 3). These scores, derived from p values, indicated the likelihood of the focus genes belonging to a network versus those obtained by chance alone, thereby eliminating the probability of their occurrence in a network to be due to noise. The network 1 with the highest score (score = 25) is comprised of gene expression, small molecule biochemistry and cancer. Other subsequent networks included network 2 (score = 19) of gene expression, cellular development, cellular growth and proliferation, and network 3 (score = 16) of antigen presentation, inflammatory response, dermatological diseases and conditions. These results implied that the altered genes were distributed among diverse networks that could be expected to the various influence on patients by H. pylori infection. Meanwhile, the significant (p<0.05) “molecular and cellular function” in IPA software was comprised of antigen presentation, cell death, gene expression, molecular transport and cellular development, while protein ubiquitination pathway was the most significant (p = 0.0124) “top canonical pathway” altered by H. pylori infection in chronic superficial gastritis.


Gene expression profiling in gastric mucosa from Helicobacter pylori-infected and uninfected patients undergoing chronic superficial gastritis.

Yang ZM, Chen WW, Wang YF - PLoS ONE (2012)

IPA network analysis of molecule interactions.The focus genes differentially expressed in this study were indicated by red symbols (up-regulated) and green symbols (down-regulated). The non-focus genes were not shown to be significant difference by the microarray analysis, and placed in the network by the Ingenuity software as intermediate molecules which were denoted by open symbols. Whereas symbols represented functional categories of the molecules are listed in the legend.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3306372&req=5

pone-0033030-g003: IPA network analysis of molecule interactions.The focus genes differentially expressed in this study were indicated by red symbols (up-regulated) and green symbols (down-regulated). The non-focus genes were not shown to be significant difference by the microarray analysis, and placed in the network by the Ingenuity software as intermediate molecules which were denoted by open symbols. Whereas symbols represented functional categories of the molecules are listed in the legend.
Mentions: To interpret differentially expressed genes of H. pylori infection in the context of biological processes, pathways and networks, IPA Core Analyses were conducted and three high scoring networks (score>15) including 82% (28/34) of differentially expressed genes were identified (Figure 3). These scores, derived from p values, indicated the likelihood of the focus genes belonging to a network versus those obtained by chance alone, thereby eliminating the probability of their occurrence in a network to be due to noise. The network 1 with the highest score (score = 25) is comprised of gene expression, small molecule biochemistry and cancer. Other subsequent networks included network 2 (score = 19) of gene expression, cellular development, cellular growth and proliferation, and network 3 (score = 16) of antigen presentation, inflammatory response, dermatological diseases and conditions. These results implied that the altered genes were distributed among diverse networks that could be expected to the various influence on patients by H. pylori infection. Meanwhile, the significant (p<0.05) “molecular and cellular function” in IPA software was comprised of antigen presentation, cell death, gene expression, molecular transport and cellular development, while protein ubiquitination pathway was the most significant (p = 0.0124) “top canonical pathway” altered by H. pylori infection in chronic superficial gastritis.

Bottom Line: The annotated genes were involved in protein metabolism, inflammatory and immunological reaction, signal transduction, gene transcription, trace element metabolism, and so on.The 82% of these genes (28/34) were categorized in three molecular interaction networks involved in gene expression, cancer progress, antigen presentation and inflammatory response.The expression data of the array hybridization was confirmed by quantitative real-time PCR assays.

View Article: PubMed Central - PubMed

Affiliation: Pi-Wei Institute, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.

ABSTRACT
Helicobacter pylori infection reprograms host gene expression and influences various cellular processes, which have been investigated by cDNA microarray using in vitro culture cells and in vivo gastric biopsies from patients of the Chronic Abdominal Complaint. To further explore the effects of H. pylori infection on host gene expression, we have collected the gastric antral mucosa samples from 6 untreated patients with gastroscopic and pathologic confirmation of chronic superficial gastritis. Among them three patients were infected by H. pylori and the other three patients were not. These samples were analyzed by a microarray chip which contains 14,112 cloned cDNAs, and microarray data were analyzed via BRB ArrayTools software and Ingenuity Pathways Analysis (IPA) website. The results showed 34 genes of 38 differentially expressed genes regulated by H. pylori infection had been annotated. The annotated genes were involved in protein metabolism, inflammatory and immunological reaction, signal transduction, gene transcription, trace element metabolism, and so on. The 82% of these genes (28/34) were categorized in three molecular interaction networks involved in gene expression, cancer progress, antigen presentation and inflammatory response. The expression data of the array hybridization was confirmed by quantitative real-time PCR assays. Taken together, these data indicated that H. pylori infection could alter cellular gene expression processes, escape host defense mechanism, increase inflammatory and immune responses, activate NF-κB and Wnt/β-catenin signaling pathway, disturb metal ion homeostasis, and induce carcinogenesis. All of these might help to explain H. pylori pathogenic mechanism and the gastroduodenal pathogenesis induced by H. pylori infection.

Show MeSH
Related in: MedlinePlus