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Hypoxia-induced human deoxyribonuclease I is a cellular restriction factor of hepatitis B virus

Abstract

Numerous human APOBEC3 cytidine deaminases have proven to be, inter alia, host cell restriction factors for retroviruses and hepadnaviruses. Although they can bind to genomic RNA and become encapsidated, they are only catalytically active on single-stranded DNA. As there are many cellular deoxyribonucleases (DNases), we hypothesized that a parallel could be struck between APOBEC3 and DNases. For human hepatitis B virus (HBV), we show that DNase I can considerably reduce the virion genome copy number from a variety of transfected or infected cells. DNASE1 is overexpressed and encapsidated in HBV particles in vitro in hypoxic environments and in vivo in cirrhotic patient livers as well as in the serum of infected patients. The use of CoCl2 and dimethyloxalylglycine, mimetic agents used to induce hypoxia by inhibiting prolyl hydroxylase enzymes that stabilize hypoxia-inducible factor (HIF)-1α, showed that the formation of HIF-1α/HIF-1β heterodimers results in the induction of DNASE1. Indeed, transfection with HIF-1α and HIF-1β expression constructs upregulated DNASE1. These findings suggest that human DNase I can impact HBV replication through the catabolism of the DNA genome within the capsid. The activity of DNases in general may explain in part the high frequency of empty or ‘light’ hepatitis B virions observed in vivo.

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The data that support the findings of this study are available from the corresponding authors on request.

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Acknowledgements

Lanzhou Institute of Biological Products Co., Ltd. is a subsidiary company of China National Biotec Group Company Limited. This work was supported by grants from the Institut Pasteur and Centre National de la Recherche Scientifique. C.H. and M.S.B. were supported by the Allocation de Recherche du Ministère de la Recherche and Ligue contre le Cancer, respectively. X.L. was supported by a stipend from the Lanzhou Institute of Biological Products Co., Ltd, subsidiary company of China National Biotec Group Company Limited and by a stipend from the Pasteur-Paris University International PhD program. V.L. was supported by the Fondation pour la Recherche Medicale (project no. ING20160435328). C.D. was supported by an EMBO Long Term Fellowship (EMBO ALTF 1428–2016). The study of patients was sponsored by the French National Agency for research on AIDS and hepatitis (ANRS). This work has been published within the framework of IdEx Université de Strasbourg and has received funding from the French State via the French National Research Agency (ANR) as part of the program ‘Investissements d’avenir’ to R.G. This work was supported by an ATIP-AVENIR starting grant to R.G. We would like to thank S. Urban for providing HepG2-NTCP cells; P. Pineau and A. Marchio for the cirrhotic liver samples; M.-L. Michel and S. Pol for serum samples; C. Neuveut, P. Moreau, P. Maillard and B. Quioc for HBV infection; Y. Jacob for the HIF-1α and HIF-1β plasmids; J. Krijnse-Locker and C. Schmitt for electron microscopy immunolabelling and V. Caval, N. Frampton and J. McKeating for helpful discussions.

Author information

S.W.-H. and J.-P.V. designed the research. C.H., X.X.L., R.S., V.T., M.S.B., V.L., C.D. and R.G. performed the experiments. C.H., X.X.L., R.S., V.T., M.S.B., V.L., C.D., S.W.-H., R.G. and J.-P.V. analysed the data. S.W.-H., R.G. and J.-P.V. wrote the paper.

Competing interests

The authors declare no competing interests.

Correspondence to Raphaël Gaudin or Jean-Pierre Vartanian.

Supplementary information

  1. Supplementary Information

    Supplementary Figures 1–7, Supplementary Tables 1 and 2, Raw Image Figures and Raw Image.

  2. Reporting Summary

  3. Supplementary Video 1

    Three-dimensional time-lapse of the crop presented in Supplementary Figure 5.

  4. Supplementary Video 2

    Three-dimensional isosurface time-lapse of the of the crop presented in Supplementary Figure 5.

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Fig. 1: DNase I constructs and activity.
Fig. 2: DNase I reduces HBV DNA levels.
Fig. 3: DNase I is incorporated within HBV particles.
Fig. 4: Hypoxia enhances DNASE1 expression and restricts HBV.
Fig. 5: Expression analysis of DNASE1 and HBV restriction in CoCl2-treated HepG2 cells.
Fig. 6: DNASE1 upregulation in vivo and HIF-1α/HIF-1β involvement.