The ALPK1/TIFA/NF-\u03baB axis links a bacterial carcinogen to R-loop-induced replication stress

Michael Bauer,Thomas F Meyer,Antonia Töpfer,Anne Müller,Jana Dobrovolná ,Xiling Shen,Pavel Janscak,Zuzana Naščáková ,Nina R Salama,Sina Bartfeld,Robert Hurwitz,Alevtina Gall ,Simon Lampart,Lennart Pfannkuch,Anders B Dohlman ,Melanie Jacobs,Achim Weber,Anca-Irina Mihai,Phil F Cheng,Mitchell P Levesque

doi:10.1038/s41467-020-18857-z

Abstract

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.

Highlights

Exposure of gastric epithelial cells to the bacterial carcinogen Helicobacter pylori causes DNA double strand breaks
To investigate whether the β-ADP-heptose/alpha-kinase 1 (ALPK1)/ TIFA signaling axis is involved in H. pylori-induced DNA damage, we took advantage of AGS gastric epithelial cells that were either proficient or deficient for ALPK1 and TIFA expression due to genetic ablation of the respective loci by CRISPR/Cas[9] technology[21]
These results indicate that the resistance of ALPK1- or TIFA-deficient AGS cells to H. pylori-induced DNA damage is due to TIFA ablation and not off-target effects of CRISPR

Summary

Introduction

Exposure of gastric epithelial cells to the bacterial carcinogen Helicobacter pylori causes DNA double strand breaks. 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-ADPheptose/ ALPK1/TIFA/NF-κB signaling. As a consequence of a large body of evidence implicating H. pylori in gastric carcinogenesis, screening programs using upper gastrointestinal tract endoscopy are in place in countries with a high gastric cancer burden, such as South Korea or Japan. These programs have allowed for early detection of gastric cancer and have reduced mortality from this disease[12].

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Conclusion