Loss of DHX36/G4R1, a G4 resolvase, drives genome instability and regulates innate immune gene expression in cancer cells

Bartosik, A. R.; Hou, P.-C.; Vaughn, J. P.; Smaldino, P. J.; Ratan, A.; Mayo, M. W.; Wang, Y.-H.

doi:10.1101/2025.01.03.631217

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bioRxiv · 10.1101/2025.01.03.631217

Loss of DHX36/G4R1, a G4 resolvase, drives genome instability and regulates innate immune gene expression in cancer cells

Bartosik, A. R.·Hou, P.-C.·Vaughn, J. P.·Smaldino, P. J.·Ratan, A.·Mayo, M. W.·Wang, Y.-H.

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Abstract

G-quadruplexes (G4s) are four-stranded alternative secondary structures formed by guanine-rich nucleic acids and are prevalent across the human genome. G4s are enzymatically resolved using specialized helicases. Previous in vitro studies showed that DEAH-box Helicase 36 (DHX36/G4R1/RHAU), has the highest specificity and affinity for G4 structures. Here, by mapping genome-wide DNA double-strand breaks (DSBs), we demonstrate that knockout (KO) of DHX36 helicase increases DSB enrichment at G4 sites and that the presence of the G4 motif is a significant mediator of genome instability at regulatory regions. The loss of DHX36 corresponds with the significant upregulation of NF-{kappa}B transcriptional programs, culminating in the production and secretion of proinflammatory cytokines. Loss of DHX36 expression results in an increase in the innate immune signaling stimulator of interferon response cGAMP interactor 1 (STING1) expression and activation of genes involved in immune response pathways. Importantly, higher levels of DHX36 mRNA expression in human B-cell acute lymphoblastic leukemia correlate with improved overall survival relative to lower expression of DHX36, highlighting its critical role in preserving genome integrity at a cellular level and in the context of cancer.

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Bartosik, A. R., Hou, P.-C., Vaughn, J. P., Smaldino, P. J., Ratan, A., Mayo, M. W., Wang, Y.-H.. 2025-01-03. Loss of DHX36/G4R1, a G4 resolvase, drives genome instability and regulates innate immune gene expression in cancer cells. https://doi.org/10.1101/2025.01.03.631217

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