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Comparative genomics of Helicobacter pylori strains of China associated with different clinical outcome.

You Y, He L, Zhang M, Fu J, Gu Y, Zhang B, Tao X, Zhang J - PLoS ONE (2012)

Bottom Line: Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China.These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems.They were also associated with the virB gene, which lies on the well-studied cag pathogenic island.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

ABSTRACT
In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90,000 probes covering six sequenced Helicobacter pylori (H. pylori) genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases.

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Comparison of eight H. pylori strains based on strain specific genes of six sequenced strains.Large variable regions were labeled with colored rectangles. Predicted gastric cancer strain specific regions were labeled with a red rectangle. General genomic variations among all strains were labeled with a green rectangle. A blue rectangle represents diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains. Corresponding coding proteins were briefly labeled at the bottom of each rectangle. GC vs SG denotes comparison between the two strains of gastric cancer and the two strains of superficial gastritis.
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pone-0038528-g004: Comparison of eight H. pylori strains based on strain specific genes of six sequenced strains.Large variable regions were labeled with colored rectangles. Predicted gastric cancer strain specific regions were labeled with a red rectangle. General genomic variations among all strains were labeled with a green rectangle. A blue rectangle represents diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains. Corresponding coding proteins were briefly labeled at the bottom of each rectangle. GC vs SG denotes comparison between the two strains of gastric cancer and the two strains of superficial gastritis.

Mentions: Comparison of eight H. pylori strains based on strain specific genes of six sequenced strains is shown in Figure 4. Twelve large variable regions are labeled with rectangles, including five red rectangles denoting predicted gastric cancer strain specific regions (DR1, 3, 4, 5, 12), three blue rectangles denoting diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains (DR 9, 10, 11), and five green rectangles denoting common variable genes among all strains (DR 1, 2, 6, 7, 8). These predicted variable genes based on strain specific genes of the six sequenced strains were listed in Table 4.


Comparative genomics of Helicobacter pylori strains of China associated with different clinical outcome.

You Y, He L, Zhang M, Fu J, Gu Y, Zhang B, Tao X, Zhang J - PLoS ONE (2012)

Comparison of eight H. pylori strains based on strain specific genes of six sequenced strains.Large variable regions were labeled with colored rectangles. Predicted gastric cancer strain specific regions were labeled with a red rectangle. General genomic variations among all strains were labeled with a green rectangle. A blue rectangle represents diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains. Corresponding coding proteins were briefly labeled at the bottom of each rectangle. GC vs SG denotes comparison between the two strains of gastric cancer and the two strains of superficial gastritis.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368837&req=5

pone-0038528-g004: Comparison of eight H. pylori strains based on strain specific genes of six sequenced strains.Large variable regions were labeled with colored rectangles. Predicted gastric cancer strain specific regions were labeled with a red rectangle. General genomic variations among all strains were labeled with a green rectangle. A blue rectangle represents diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains. Corresponding coding proteins were briefly labeled at the bottom of each rectangle. GC vs SG denotes comparison between the two strains of gastric cancer and the two strains of superficial gastritis.
Mentions: Comparison of eight H. pylori strains based on strain specific genes of six sequenced strains is shown in Figure 4. Twelve large variable regions are labeled with rectangles, including five red rectangles denoting predicted gastric cancer strain specific regions (DR1, 3, 4, 5, 12), three blue rectangles denoting diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains (DR 9, 10, 11), and five green rectangles denoting common variable genes among all strains (DR 1, 2, 6, 7, 8). These predicted variable genes based on strain specific genes of the six sequenced strains were listed in Table 4.

Bottom Line: Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China.These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems.They were also associated with the virB gene, which lies on the well-studied cag pathogenic island.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

ABSTRACT
In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90,000 probes covering six sequenced Helicobacter pylori (H. pylori) genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases.

Show MeSH
Related in: MedlinePlus