Letter | Published:

HIV-1 evades innate immune recognition through specific cofactor recruitment

Nature volume 503, pages 402405 (21 November 2013) | Download Citation

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Abstract

Human immunodeficiency virus (HIV)-1 is able to replicate in primary human macrophages without stimulating innate immunity despite reverse transcription of genomic RNA into double-stranded DNA, an activity that might be expected to trigger innate pattern recognition receptors. We reasoned that if correctly orchestrated HIV-1 uncoating and nuclear entry is important for evasion of innate sensors then manipulation of specific interactions between HIV-1 capsid and host factors that putatively regulate these processes should trigger pattern recognition receptors and stimulate type 1 interferon (IFN) secretion. Here we show that HIV-1 capsid mutants N74D and P90A, which are impaired for interaction with cofactors cleavage and polyadenylation specificity factor subunit 6 (CPSF6) and cyclophilins (Nup358 and CypA), respectively1,2, cannot replicate in primary human monocyte-derived macrophages because they trigger innate sensors leading to nuclear translocation of NF-κB and IRF3, the production of soluble type 1 IFN and induction of an antiviral state. Depletion of CPSF6 with short hairpin RNA expression allows wild-type virus to trigger innate sensors and IFN production. In each case, suppressed replication is rescued by IFN-receptor blockade, demonstrating a role for IFN in restriction. IFN production is dependent on viral reverse transcription but not integration, indicating that a viral reverse transcription product comprises the HIV-1 pathogen-associated molecular pattern. Finally, we show that we can pharmacologically induce wild-type HIV-1 infection to stimulate IFN secretion and an antiviral state using a non-immunosuppressive cyclosporine analogue. We conclude that HIV-1 has evolved to use CPSF6 and cyclophilins to cloak its replication, allowing evasion of innate immune sensors and induction of a cell-autonomous innate immune response in primary human macrophages.

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Change history

  • 20 November 2013

    Figure 3 was corrected and changes were made to the Acknowledgements section.

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ArrayExpress

Protein Data Bank

Data deposits

Structural coordinates have been deposited under PDB accession code 4IPZ. Microarray data are available from the EBI Array Express repository under accession no. E-MTAB-1437.

References

  1. 1.

    et al. Flexible use of nuclear import pathways by HIV-1. Cell Host Microbe 7, 221–233 (2010)

  2. 2.

    et al. HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency. PLoS Pathog. 7, e1002439 (2011)

  3. 3.

    et al. CPSF6 defines a conserved capsid interface that modulates HIV-1 replication. PLoS Pathog. 8, e1002896 (2012)

  4. 4.

    et al. Human immunodeficiency virus type 1 capsid mutation N74D alters cyclophilin A dependence and impairs macrophage infection. J. Virol. 86, 4708–4714 (2012)

  5. 5.

    et al. HIV-1 infection of macrophages is dependent on evasion of innate immune cellular activation. AIDS 23, 2255–2263 (2009)

  6. 6.

    , & Restriction of lentivirus in monkeys. Proc. Natl Acad. Sci. USA 99, 11920–11925 (2002)

  7. 7.

    , , , & Measurement of human immunodeficiency virus type 1 preintegration transcription by using Rev-dependent Rev-CEM cells reveals a sizable transcribing DNA population comparable to that from proviral templates. J. Virol. 83, 8662–8673 (2009)

  8. 8.

    , , , & Small-molecule inhibition of human immunodeficiency virus type 1 infection by virus capsid destabilization. J. Virol. 85, 542–549 (2011)

  9. 9.

    et al. HIV capsid is a tractable target for small molecule therapeutic intervention. PLoS Pathog. 6, e1001220 (2010)

  10. 10.

    , , , & Distinct sequence motifs within the 68-kDa subunit of cleavage factor Im mediate RNA binding, protein-protein interactions, and subcellular localization. J. Biol. Chem. 279, 35788–35797 (2004)

  11. 11.

    et al. HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2. PLoS Pathog. 7, e1001313 (2011)

  12. 12.

    , , , & Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 339, 786–791 (2013)

  13. 13.

    et al. Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses. Science 341, 903–906 (2013)

  14. 14.

    et al. A mitochondrial-targeted cyclosporin A with high binding affinity for cyclophilin D yields improved cytoprotection of cardiomyocytes. Biochem. J. 441, 901–907 (2012)

  15. 15.

    , , , & Cyclosporin A inhibits hepatitis C virus replication and restores interferon-alpha expression in hepatocytes. Transpl. Inf. Dis. 13, 24–32 (2011)

  16. 16.

    , , , & The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1. Nature Immunol. 11, 1005–1013 (2010)

  17. 17.

    et al. A cryptic sensor for HIV-1 activates antiviral innate immunity in dendritic cells. Nature 467, 214–217 (2010)

  18. 18.

    et al. Primary human immunodeficiency virus type 2 (HIV-2) isolates, like HIV-1 isolates, frequently use CCR5 but show promiscuity in coreceptor usage. J. Virol. 73, 2343–2349 (1999)

  19. 19.

    , , , & Antiretroviral potential of human tripartite motif-5 and related proteins. Virology 353, 396–409 (2006)

  20. 20.

    et al. HIV-1 capsid-targeting domain of cleavage and polyadenylation specificity factor 6. J. Virol. 86, 3851–3860 (2012)

  21. 21.

    , & mRNA 3′ end processing and more–multiple functions of mammalian cleavage factor I-68. Wiley interdisciplinary reviews. RNA 2, 79–91 (2011)

  22. 22.

    , & The structure of human cleavage factor Im hints at functions beyond UGUA-specific RNA binding: a role in alternative polyadenylation and a potential link to 5′ capping and splicing. RNA Biol. 8, 748–753 (2011)

  23. 23.

    et al. A carboxy-terminally truncated human CPSF6 lacking residues encoded by exon 6 inhibits HIV-1 cDNA synthesis and promotes capsid disassembly. J. Virol. 87, 7726–7736 (2013)

  24. 24.

    , , , & Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo. Nature Biotechnol. 15, 871–875 (1997)

  25. 25.

    et al. In vivo gene delivery and stable transduction of non-dividing cells by a lentiviral vector. Science 272, 263–267 (1996)

  26. 26.

    et al. Characterization of novel safe lentiviral vectors derived from simian immunodeficiency virus (SIVmac251) that efficiently transduce mature human dendritic cells. Gene Ther. 7, 1613–1623 (2000)

  27. 27.

    et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34, 374–378 (2003)

  28. 28.

    et al. Curating the innate immunity interactome. BMC Syst. Biol. 4, 117 (2010)

  29. 29.

    , & A quantitative assay for HIV DNA integration in vivo. Nature Med. 7, 631–634 (2001)

  30. 30.

    , & STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity. Nature 461, 788–792 (2009)

  31. 31.

    Collaborative Computational Project, number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  32. 32.

    , , & X-ray structure of a monomeric cyclophilin A-cyclosporin A crystal complex at 2.1 Å resolution. J. Mol. Biol. 234, 1119–1130 (1993)

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Acknowledgements

We are grateful to J. W. Chin, S. Goodbourn, K. Lee, O. Perisic and V. KewalRamani for reagents and advice. This work was funded by Wellcome Trust Senior Fellowship 090940 to G.J.T., the Medical Research Council, an MRC Confidence in Concept Award to G.J.T. and D.S. and the National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health.

Author information

Author notes

    • Mahdad Noursadeghi
    •  & Greg J. Towers

    These authors contributed equally to this work.

Affiliations

  1. University College London, Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 90 Gower Street, London WC1E 6BT, UK

    • Jane Rasaiyaah
    • , Choon Ping Tan
    • , Adam J. Fletcher
    • , Caroline Blondeau
    • , Laura Hilditch
    • , Mahdad Noursadeghi
    •  & Greg J. Towers
  2. Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK

    • Amanda J. Price
    • , David A. Jacques
    •  & Leo C. James
  3. Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK

    • David L. Selwood

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Contributions

J.R., C.P.T., A.J.F., D.L.S., M.N. and G.J.T. designed the study. J.R. performed all experiments in MDM, C.P.T. performed cGAMP and immunostimulatory RNA assays, A.J.F. performed CPSF6 experiments in HeLa cells. A.J.P. solved the structure of SmBz-CsC in complex with CypA and L.H. performed the TRIMCyp experiments. J.R., A.J.F., A.J.P., L.H., D.A.J., L.C.J., M.N. and G.J.T. analysed the data. A.J.F. and C.B. generated constructs and D.L.S. synthesized SmBz-CsA. J.R., M.N. and G.J.T. wrote the manuscript.

Competing interests

J.R., L.C.J., D.S. and G.J.T. are inventors on a patent claiming the anti-HIV activity of SmBz-CsA.

Corresponding authors

Correspondence to Mahdad Noursadeghi or Greg J. Towers.

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DOI

https://doi.org/10.1038/nature12769

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