BACKGROUND: Helicobacter pylori, a gram-negative bacterium associated with a spectrum of benign and malignant gastric conditions, is one of the most genetically variable pathogens. Its genome encodes a large number of DNA methyltransferases targeting specific motif sequences of ∼4-15 bp. DNA base modifications epigenetically regulate gene expression and genome-wide methylation profiles (methylomes) have been hypothesized to be associated with virulence. A limited number of H. pylori methylomes have been published to date, precluding meaningful analyses of clinical correlates.

METHODS: We sequenced 30 H. pylori clinical isolates from Mexico City using Pacific Biosciences’ Single Molecule Real-Time (SMRT) technology, a unique platform that simultaneously determines a wide range of DNA base modifications. The resulting methylome data were compared for the 15 strains from gastric cancer cases vs. the 15 from non-atrophic gastritis controls.

RESULTS: All 30 strains exhibited high levels of DNA methylation throughout their genomes. Three types of base modification were detected: N6-methyladenine (m6A), N4-methylcytosine (m4C) and 5-methylcytosine (m5C). m6A was more common than m4C, and m5C was rare. Over 100 different motifs were detected, including many novel motifs not found in the three reference strains. For most methylated motifs, >95% of all occurrences in a given genome were methylated. Individual strains had between 14 and 28 different motifs. Some of the methylated motifs were conserved across all (e.g., Cm6ATG) or almost all (e.g., Gm6ACT) strains, but the majority were found in only one or two strains. Two conserved motifs, GTm6AC and GTNNm6AC, were significantly (P<0.05) more common in cancer cases than controls. CONCLUSIONS: The H. pylori methylome varies widely across strains, in concert with the high plasticity of its genome. Epigenetic modifications may modulate bacterial pathogenicity. These intriguing observations warrant replication with larger numbers and multiple populations in different geographic areas. The inferred novel methyltransferases remain to be identified and functionally characterized. This report greatly increases the number of H. pylori strains with defined methylomes, and represents the first effort to associate these features with clinical outcome. Availability of these genomic and epigenomic data will enhance understanding of H. pylori pathogenesis.

Citation Format: M. Constanza Camargo, Javier Torres, Jay V. Solnick, Castle Raley, Dylan Storey, Marina Becker, Roberto Torres, Allison Weis, Carol Huang, Nguyet Kong, Lori M. Hanson, Yongmei Zhao, Xiongfong Chen, Bao Tran, Bart Weimer, Charles S. Rabkin. DNA methylation profiles of Helicobacter pylori strains from patients with gastric cancer and gastritis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3438.