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. Access through your institution Buy or subscribe This is a preview of subscription

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* Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS THE DNA GLYCOSYLASE NEIL2 IS PROTECTIVE DURING SARS-COV-2

INFECTION Article Open access 09 December 2023 AVIAN INFLUENZA VIRUSES SUPPRESS INNATE IMMUNITY BY INDUCING _TRANS_-TRANSCRIPTIONAL READTHROUGH _VIA_ SSU72 Article Open access 24 March 2022

SARS-COV-2 INFECTION INDUCES DNA DAMAGE, THROUGH CHK1 DEGRADATION AND IMPAIRED 53BP1 RECRUITMENT, AND CELLULAR SENESCENCE Article Open access 09 March 2023 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 1–5. Raw data from all other figures

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host factor. _Cell Rep._ 20, 1503–1512 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar  Download references 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. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA Benjamin S. Chambers, 

Brook E. Heaton, Rebekah E. Dumm & Nicholas S. Heaton * Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA Keiko Rausch & Sara Cherry * Department of

Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA Jennifer R. Hamilton Authors * Benjamin S. Chambers View author publications You can also search for this

author inPubMed Google Scholar * Brook E. Heaton View author publications You can also search for this author inPubMed Google Scholar * Keiko Rausch View author publications You can also

search for this author inPubMed Google Scholar * Rebekah E. Dumm View author publications You can also search for this author inPubMed Google Scholar * Jennifer R. Hamilton View author

publications You can also search for this author inPubMed Google Scholar * Sara Cherry View author publications You can also search for this author inPubMed Google Scholar * Nicholas S.

Heaton View author publications You can also search for this author inPubMed Google Scholar 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. ETHICS DECLARATIONS COMPETING INTERESTS Duke University has filed a

provisional patent for targeting DNA MMR as a method to enhance the growth of influenza vaccine strains. ADDITIONAL INFORMATION PUBLISHER’S NOTE: Springer Nature remains neutral with regard

to jurisdictional claims in published maps and institutional affiliations. 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. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE

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 Download citation * Received: 03 December 2018 * Accepted: 07 June 2019 * Published: 29 July 2019 * Issue Date: November 2019 *

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