Article Text

PDF

Original Article
Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments

Abstract

Objective Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease.

Design Whole genome sequencing of genetically related H. pylori strains that differ in virulence and targeted H. pylori sequencing following prolonged exposure of bacteria to in vitro carcinogenic conditions were performed.

Results A total of 180 unique single nucleotide polymorphisms (SNPs) were identified among the collective genomes when compared with a reference H. pylori genome. Importantly, common SNPs were identified in isolates harvested from iron-depleted and high salt carcinogenic microenvironments, including an SNP within fur (FurR88H). To investigate the direct role of low iron and/or high salt, H. pylori was continuously cultured in vitro under low iron or high salt conditions to assess fur genetic variation. Exposure to low iron or high salt selected for the FurR88H variant after only 5 days. To extend these results, fur was sequenced in 339 clinical H. pylori strains. Among the isolates examined, 17% (40/232) of strains isolated from patients with premalignant lesions harboured the FurR88H variant, compared with only 6% (6/107) of strains from patients with non-atrophic gastritis alone (p=0.0034).

Conclusion These results indicate that specific genetic variation arises within H. pylori strains during in vivo adaptation to conditions conducive for gastric carcinogenesis.

  • Helicobacter pylori
  • gastric cancer
  • iron deficiency
  • high salt

This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/

Statistics from Altmetric.com

Footnotes

  • Contributors JMN contributed to the study design, performed experiments, gathered and analysed data, and drafted the manuscript. AC generated and analysed whole genome sequences. JTL generated and provided sequence data from Helicobacter pylori strains harvested from gerbils maintained on regular or high salt diets. JRG assisted with all animal experiments and isolation of in vivo-adapted H. pylori strains. MBP provided all patient information from the two Colombian patient cohorts and clinical H. pylori isolates from these subjects. MW and SL generated and analysed whole genome sequences. ACB and KTW provided feedback on the manuscript. TLC contributed to the study design and provided sequence data from H. pylori strains harvested from gerbils maintained on regular or high salt diets. SM contributed to the study design and the whole genome sequence analysis. DAI contributed to the study design, analysed sequence data, and helped with drafting and editing the manuscript. RMP contributed to the study design and helped with drafting and editing the manuscript.

  • Competing interests None declared.

  • Patient consent Obtained

  • Ethics approval Institutional Review Board, Vanderbilt University Medical Center.

  • Provenance and peer review Not commissioned; externally peer reviewed.

Request permissions

If you wish to reuse any or all of this article please use the link below which will take you to the Copyright Clearance Center’s RightsLink service. You will be able to get a quick price and instant permission to reuse the content in many different ways.