Exposure of gastric epithelial cells to the bacterial carcinogen Helicobacter pylori causes DNA double strand breaks. Here, we show that H. pylori-induced DNA damage occurs co-transcriptionally in S-phase cells that activate NF-κB signaling upon innate immune recognition of the lipopolysaccharide biosynthetic intermediate β-ADP-heptose by the ALPK1/TIFA signaling pathway. DNA damage depends on the bi-functional RfaE enzyme and the Cag pathogenicity island of H. pylori, is accompanied by replication fork stalling and can be observed also in primary cells derived from gastric organoids. Importantly, H. pylori-induced replication stress and DNA damage depend on the presence of co-transcriptional RNA/DNA hybrids (R-loops) that form in infected cells during S-phase as a consequence of β-ADP-heptose/ ALPK1/TIFA/NF-κB signaling. H. pylori resides in close proximity to S-phase cells in the gastric mucosa of gastritis patients. Taken together, our results link bacterial infection and NF-κB-driven innate immune responses to R-loop-dependent replication stress and DNA damage.

Biomedical Engineering Duke University Durham NC USA

Comprehensive Cancer Center Zurich Zurich Switzerland

Department of Dermatology University Hospital Zurich Zurich Switzerland

Department of Pathology and Molecular Pathology University Hospital Zurich and University of Zurich Zurich Switzerland

Division of Human Biology Fred Hutchinson Cancer Research Center Seattle WA USA

Faculty of Science Charles University Prague 128 00 Prague Czech Republic

Institute of Molecular Cancer Research University of Zurich 8057 Zurich Switzerland

Institute of Molecular Genetics Academy of Sciences of the Czech Republic 142 20 Prague Czech Republic

Max Planck Institute for Infection Biology Department of Molecular Biology 10117 Berlin Germany

Research Center for Infectious Diseases Institute for Molecular Infection Biology University of Würzburg 97080 Würzburg Germany

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