AAV Kills Dividing Cells by Depleting PARP1 and Other DNA Damage Response Proteins

Friese, S.; Zai, J.; Luzbetak, G.; Khanna, N.; Gesperger, J.; Liu, C.-H.; Roos, W.; Al-Rahahleh, R.; Willardson, M.; Yang, F.; Fu, D.; Han, Y.; Lintag, N.; Saykham, J.; Le, J.; Al-Delaimy, E.; Soutipan, N.; Duong, E.; Rich, J.; Marchetto, M. C.; Rosenfeld, M.; Sobol, R. W.; Shtrahman, M.

doi:10.1101/2025.10.14.682484

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bioRxiv · 10.1101/2025.10.14.682484

AAV Kills Dividing Cells by Depleting PARP1 and Other DNA Damage Response Proteins

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Abstract

Recombinant adeno-associated virus (rAAV) is a replication-defective viral vector used in hundreds of human gene therapy trials, resulting in five FDA-approved therapies. Despite this success, rAAV-based gene therapies suffer from dose-limiting toxicities, resulting in several severe adverse reactions, including death. Previously, we discovered that rAAV rapidly kills mouse NPCs in vitro and in vivo. This vector contains a minimal genome comprised of 145-base pair inverted terminal repeats (ITRs) with a T-shaped hairpin structure that appears to be necessary and sufficient for this toxicity. However, the mechanism for AAV ITR toxicity is not known, and there have been few attempts to engineer ITRs to attenuate rAAV toxicity. In the current study, we explore the molecular mechanisms that drive dose-dependent rAAV toxicity in dividing human NPCs (hNPCs) and test whether disrupting these mechanisms mitigates this toxicity. Recombinant AAV infection induces aberrant cell cycle progression with activation of the ATM /CHK1/CHK2 pathway and expression of the DNA damage markers {gamma}H2AX and 53BP1. Affinity-based proteomics indicate that AAV ITRs bind to Poly-(ADP-Ribose)polymerase 1 (PARP1) and other DNA damage response (DDR) proteins involved in single-strand break repair (SSBR). Recombinant AAV infection attenuates poly-(ADP-ribose) (PAR) formation and mimics the antiproliferative effects of pharmacological PARP inhibitors used in cancer therapy. Moreover, treatment of hNPCs with PARP inhibitors is sufficient to reproduce many features of rAAV-induced toxicity. Finally, we demonstrate that eliminating the T-shaped hairpin within the AAV ITR reduces binding to SSBR proteins and the resulting rAAV toxicity. These findings suggest that rAAV infection induces replication stress and cell death in dividing hNPCs by functionally depleting PARP1 and other DDR proteins that are essential for DNA replication. This work fills substantial gaps in the understanding of the mechanisms of rAAV toxicity and has important implications for the development of safer rAAV-based human gene therapies. One Sentence SummaryThe rAAV genome binds to and depletes PARP1 and other SSBR proteins that are essential for DNA replication, resulting in DNA double stranded breaks, checkpoint activation, and cell death in dividing cells.

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Friese, S., Zai, J., Luzbetak, G., Khanna, N., Gesperger, J., Liu, C.-H., Roos, W., Al-Rahahleh, R., Willardson, M., Yang, F., Fu, D., Han, Y., Lintag, N., Saykham, J., Le, J., Al-Delaimy, E., Soutipan, N., Duong, E., Rich, J., Marchetto, M. C., Rosenfeld, M., Sobol, R. W., Shtrahman, M.. 2025-10-15. AAV Kills Dividing Cells by Depleting PARP1 and Other DNA Damage Response Proteins. https://doi.org/10.1101/2025.10.14.682484

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