Limits...
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.

Show MeSH

Related in: MedlinePlus

Comparison of HLJ005, HLJ038, and 26695 based on 0–100 kb of p12 genome.A. Comparison between HLJ005 and 26695. B. Comparison between HLJ038 and 26695. C. Comparison between HLJ038 and HLJ005. Green spots show inferred loss while orange dots show no changes in the original data. Red spots show inferred increase. The red rectangle indicates the predicted 5.2 kb absent region both in gastric cancer strain HLJ038 and HLJ005 based on the 0–100 kb of the reference P12 chromosome.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3368837&req=5

pone-0038528-g002: Comparison of HLJ005, HLJ038, and 26695 based on 0–100 kb of p12 genome.A. Comparison between HLJ005 and 26695. B. Comparison between HLJ038 and 26695. C. Comparison between HLJ038 and HLJ005. Green spots show inferred loss while orange dots show no changes in the original data. Red spots show inferred increase. The red rectangle indicates the predicted 5.2 kb absent region both in gastric cancer strain HLJ038 and HLJ005 based on the 0–100 kb of the reference P12 chromosome.

Mentions: In order to test whether the established H. pylori microarray analysis system can accurately predict genomic distinction, we first analyzed strains 26695, HLJ005, and HLJ038 based on strain specific genes and 0–100 kb of the reference P12 genome sequence. As shown in Figure 1, six segments on the X-axis represent strain specific genes of the six sequenced genomes. Probes of segment one are strain specific genes of 26695. When comparing the hybridization signal of gastric cancer strain HLJ005 to 26695 with the web tool ADaCGH, almost all of these genes were predicted to be absent in HLJ005 (Figure 1 A). The same pattern was found in another gastric cancer strain HLJ038 (Figure 1 B).When comparing HLJ005 and HLJ038, only some minor variable probes were found in the six segments (Figure 1 C). These analyses indicate that this custom designed microarray platform accurately predicts gene absence or presence in different clinical H. pylori isolates. This was further validated by PCR to confirm a predicted 5.2 kb absent region both in gastric cancer strain HLJ038 and HLJ005 based on the 0–100 kb of the reference P12 chromosome (Figure 2).


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 HLJ005, HLJ038, and 26695 based on 0–100 kb of p12 genome.A. Comparison between HLJ005 and 26695. B. Comparison between HLJ038 and 26695. C. Comparison between HLJ038 and HLJ005. Green spots show inferred loss while orange dots show no changes in the original data. Red spots show inferred increase. The red rectangle indicates the predicted 5.2 kb absent region both in gastric cancer strain HLJ038 and HLJ005 based on the 0–100 kb of the reference P12 chromosome.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0038528-g002: Comparison of HLJ005, HLJ038, and 26695 based on 0–100 kb of p12 genome.A. Comparison between HLJ005 and 26695. B. Comparison between HLJ038 and 26695. C. Comparison between HLJ038 and HLJ005. Green spots show inferred loss while orange dots show no changes in the original data. Red spots show inferred increase. The red rectangle indicates the predicted 5.2 kb absent region both in gastric cancer strain HLJ038 and HLJ005 based on the 0–100 kb of the reference P12 chromosome.
Mentions: In order to test whether the established H. pylori microarray analysis system can accurately predict genomic distinction, we first analyzed strains 26695, HLJ005, and HLJ038 based on strain specific genes and 0–100 kb of the reference P12 genome sequence. As shown in Figure 1, six segments on the X-axis represent strain specific genes of the six sequenced genomes. Probes of segment one are strain specific genes of 26695. When comparing the hybridization signal of gastric cancer strain HLJ005 to 26695 with the web tool ADaCGH, almost all of these genes were predicted to be absent in HLJ005 (Figure 1 A). The same pattern was found in another gastric cancer strain HLJ038 (Figure 1 B).When comparing HLJ005 and HLJ038, only some minor variable probes were found in the six segments (Figure 1 C). These analyses indicate that this custom designed microarray platform accurately predicts gene absence or presence in different clinical H. pylori isolates. This was further validated by PCR to confirm a predicted 5.2 kb absent region both in gastric cancer strain HLJ038 and HLJ005 based on the 0–100 kb of the reference P12 chromosome (Figure 2).

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