Cancer-related genetic variants ofHelicobacter pyloristrains determined using gastric wash-based whole-genome analysis with single-molecule real-time technology

Helicobacter pylori(H.pylori) are a primary factor in the pathogenesis of gastric cancer (GC); GC ranks third among cancer-related mortality. A clear understanding of theH.pylorigenome factors underlying GC is necessary to develop more effective methods to prevent GC. A single-molecule real-time DNA sequencing-basedH.pylorigenome-wide association study analysis was performed using theH.pylorigenome present in five early-stage GC (EGC) and five non-GC clinical DNA samples recovered from gastric washes. A total of 275 genes with 702 nucleotide variants (NVs) were found to be common to three or more patients with EGC but no non-GC patients (single-NV: 654/702, 93.2%; multi-NV: 40/702, 5.7%; deletion: 3/702, 0.4%; insertion: 3/702, 0.7%). Gene ontology analysis ofH.pylorirevealed that genes involved in the mitochondrial electron transport system, glycolytic processes and the TCA cycle were highly enriched. Cancer-related NVs were most frequently found in a member of theHelicobacterouter membrane protein family,hopL. In particular, one of the NVs inhopLwas a novel six-nucleotide insertion (1159095^1159096, TACTTC); this mutant was detected more frequently in a validation set of 50 additional EGC samples (22/50, 44.0%) than in 18 non-GC samples (3/18, 16.7%,P= .04). These results suggest that thehopLvariant is associated with the development of GC and may serve as a genetic biomarker ofH.pylorivirulence and GC risk. Our assay can serve as a potent tool to expand our understanding of bacteria-associated tumorigenesis.

Automated summary

H.pylori plays a key role in gastric cancer development, with specific genetic variations identified in genes related to the mitochondrial electron transport system, glycolytic processes, and the TCA cycle. A novel mutation in the Helicobacter outer membrane protein family member hopL was found to be associated with gastric cancer development, indicating its potential as a genetic biomarker for H.pylori virulence and gastric cancer risk.