Helicobacter pylori infection induces DNA breaks at replication-coupled fragile sites by inducing dNTP depletion in CagA-independent manner

Helicobacter pylori (H.pylori) infection is a significant risk factor for gastric cancer (GC) development. A growing body of evidence suggests a causal link between infection with H.pylori and increased DNA breakage in the host cells. While several mechanisms have been proposed for this damage, their relative impact on the overall bacterial genotoxicity is unknown. Moreover, the link between the formation of DNA damage following infection and the emergence of cancerous structural variants (SV) in the genome of infected cells remained unexplored. To resolve these gaps, we constructed high-resolution map of genomic H.pylori-induced recurrent break sites. Our data indicated that these sites are ubiquitous across cell types, localized at replication-related fragile sites, and their breakage is dependent on replication. Consistent with that, we found that H.pylori inflicts nucleotide depletion, and that rescuing the nucleotide pool largely reduced H.pylori-induced DNA breaks. Intriguingly, we found that this genotoxic mechanism operates independently of the H.pylori virulence factor, CagA, which was previously implicated in increasing DNA damage by downregulating the DNA damage response. Finally, we show that sites of recurrent H.pylori-mediated breaks coincide with chromosomal deletions observed in patients with intestinal-type GC, and that this link potentially elucidates the persistent transcriptional alterations observed in cancer driver genes. These findings establish the link between H.pylori genotoxicity, and its oncogenic potential. Overall design: 14 samples of END-seq profile: H.pylori infected (3 samples) and uninfected (3 samples) human gastric cell line AGS, and H.pylori infected (6 samples) and uninfected (6 samples) mouse pre-B vAbl cell line, treated or untreated with STI-571 (3 each).