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DNA mismatch repair is required for the host innate response and controls cellular fate after influenza virus infection

Abstract

Despite the cytopathic nature of influenza A virus (IAV) replication, we recently reported that a subset of lung epithelial club cells is able to intrinsically clear the virus and survive infection. However, the mechanisms that drive cell survival during a normally lytic infection remained unclear. Using a loss-of-function screening approach, we discovered that the DNA mismatch repair (MMR) pathway is essential for club cell survival of IAV infection. Repair of virally induced oxidative damage by the DNA MMR pathway not only allowed cell survival of infection, but also facilitated host gene transcription, including the expression of antiviral and stress response genes. Enhanced viral suppression of the DNA MMR pathway prevented club cell survival and increased the severity of viral disease in vivo. Altogether, these results identify previously unappreciated roles for DNA MMR as a central modulator of cellular fate and a contributor to the innate antiviral response, which together control influenza viral disease severity.

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Fig. 1: NCI-H441 cells survive direct infection with influenza A virus.
Fig. 2: An siRNA screen of the druggable genome reveals host factors that control H441 cell survival during IAV infection.
Fig. 3: DNA MMR genes are important for survival and their expression is maintained in H441 cells during infection.
Fig. 4: DNA MMR activity remains high in H441 cells allowing repair of virally induced ROS-mediated DNA damage.
Fig. 5: Loss of DNA MMR activity reduces the innate antiviral transcriptional response against influenza A virus.
Fig. 6: DNA MMR is required for cellular survival and protection from virulence in mice.

Data availability

The raw RNA-seq data files from Fig. 5i–k are available at NCBI GEO (series GSE130189). The raw data for Figs. 2b–d, 3d and 5i–k are available in Supplementary Tables 15. Raw data from all other figures and unique materials, including viruses and plasmids, are available from the corresponding authors upon request.

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Acknowledgements

We would like to thank H. Bogerd and B. Cullen (Duke University) for their help with the amiRNA northern blots. We would like to thank P. Palese (Mt. Sinai) for support and reagents during preliminary optimization experiments. We would also like to thank B. tenOever (Mt. Sinai) for his help in designing the amiRNA-expressing viruses. We are also grateful for contributions made by H. Froggatt (Duke University) in researching the literature on other pathogens that downregulate DNA MMR. The RNA-seq mapping pipeline was developed by David Sachs. N.S.H. is partially supported by NIH K22-AI116509-01, R21-AI133444-01, R01-HL142985, R01-AI137031 and the Duke School of Medicine Whitehead Scholarship. B.S.C. is supported by NIH training grant T32-CA009111. R.E.D. is supported by NIH training grant T32-GM007184-41. S.C. is supported by NIH grants R01AI074951, R01AI140539 and R01AI122749, and is a recipient of the Burroughs Wellcome Investigators in the Pathogenesis of Infectious Disease Award.

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Contributions

B.S.C., S.C. and N.S.H. designed the study and experiments. B.S.C. generated many of the reagents and performed and analysed the majority of the biochemical and mouse experiments. B.E.H. performed some of the interferon gene expression experiments. K.R. and S.C. performed and analysed the siRNA screen data. R.E.D. performed and analysed the phospho-H2AX and ALI culture experiments. J.R.H. and N.S.H. generated the Cre-reporter assays and optimized screening conditions. N.S.H. performed and analysed the 8-OHdG experiment, most of the screen validation experiments and most of the experiments characterizing H441 cells as models for cell survival. B.S.C., S.C. and N.S.H. wrote the manuscript.

Corresponding authors

Correspondence to Sara Cherry or Nicholas S. Heaton.

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Duke University has filed a provisional patent for targeting DNA MMR as a method to enhance the growth of influenza vaccine strains.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–7.

Reporting Summary

Supplementary Table 1

Average Z-scores of all genes tested in both replicates of the primary siRNA screen, related to Fig. 2b,c.

Supplementary Table 2

Validation siRNA sequence information and results of statistical analysis of secondary siRNA screen, related to Figs. 2d and 2g.

Supplementary Table 3

Relative mRNA levels of DNA MMR genes at 9 h postinfection with WT PR8 in A549 and H441 cells compared to mock controls, related to Fig. 3d.

Supplementary Table 4

Raw read counts for all genes detected in RNA-seq of WT PR8-infected H441 cells with control or DNA MMR knockdown, related to Fig. 5i–k and Supplementary Fig. 4.

Supplementary Table 5

RNA-seq data and analysis for all genes induced >5-fold in WT PR8-infected H441 cells, related to Fig. 5i–k.

Supplementary Table 6

List of primers used for RT–qPCR analyses, related to Figs. 3d, 5c and 5l–o.

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Chambers, B.S., Heaton, B.E., Rausch, K. et al. DNA mismatch repair is required for the host innate response and controls cellular fate after influenza virus infection. Nat Microbiol 4, 1964–1977 (2019). https://doi.org/10.1038/s41564-019-0509-3

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