Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host

Abstract

Bats are special in their ability to host emerging viruses. As the only flying mammal, bats endure high metabolic rates yet exhibit elongated lifespans. It is currently unclear whether these unique features are interlinked. The important inflammasome sensor, NLR family pyrin domain containing 3 (NLRP3), has been linked to both viral-induced and age-related inflammation. Here, we report significantly dampened activation of the NLRP3 inflammasome in bat primary immune cells compared to human or mouse counterparts. Lower induction of apoptosis-associated speck-like protein containing a CARD (ASC) speck formation and secretion of interleukin-1β in response to both ‘sterile’ stimuli and infection with multiple zoonotic viruses including influenza A virus (−single-stranded (ss) RNA), Melaka virus (PRV3M, double-stranded RNA) and Middle East respiratory syndrome coronavirus (+ssRNA) was observed. Importantly, this reduction of inflammation had no impact on the overall viral loads. We identified dampened transcriptional priming, a novel splice variant and an altered leucine-rich repeat domain of bat NLRP3 as the cause. Our results elucidate an important mechanism through which bats dampen inflammation with implications for longevity and unique viral reservoir status.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Activation of the NLRP3 inflammasome is dampened in bat PBMCs, BMDMs and BMDCs.
Fig. 2: Transcriptional priming of bat NLRP3 is dampened independent of TLRs.
Fig. 3: The function of all four bat NLRP3 isoforms, but not ASC, is reduced.
Fig. 4: NLRP3 isoform activity in bat cells from both major bat lineages is dampened.
Fig. 5: Bat NLRP3-mediated inflammation in immune cells is dampened in response to IAV, PRV3M and MERS-CoV infection.

Similar content being viewed by others

Data availability

The data supporting the findings of this study are available from the corresponding authors upon request. RNA–seq data used in this study have been deposited in the NCBI Sequence Read Archive (SRR8382151). The bat NLRP3 sequences generated in this study have been deposited in GenBank under accession numbers MK355440MK355443. Supplementary figures and tables are provided in the Supplementary Information.

References

  1. Leroy, E. M. et al. Fruit bats as reservoirs of Ebola virus. Nature 438, 575–576 (2005).

    Article  CAS  Google Scholar 

  2. Clayton, B. A., Wang, L. F. & Marsh, G. A. Henipaviruses: an updated review focusing on the pteropid reservoir and features of transmission. Zoonoses Public Health 60, 69–83 (2013).

    Article  CAS  Google Scholar 

  3. Li, W. et al. Bats are natural reservoirs of SARS-like coronaviruses. Science 310, 676–679 (2005).

    Article  CAS  Google Scholar 

  4. Mohd, H. A., Al-Tawfiq, J. A. & Memish, Z. A. Middle East respiratory syndrome coronavirus (MERS-CoV) origin and animal reservoir. Virol. J. 13, 87 (2016).

    Article  Google Scholar 

  5. Cameron, M. J., Bermejo-Martin, J. F., Danesh, A., Muller, M. P. & Kelvin, D. J. Human immunopathogenesis of severe acute respiratory syndrome (SARS). Virus Res. 133, 13–19 (2008).

    Article  CAS  Google Scholar 

  6. Liu, X. et al. Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus. Genome Biol. 18, 4 (2017).

    Article  Google Scholar 

  7. Totura, A. L. & Baric, R. S. SARS coronavirus pathogenesis: host innate immune responses and viral antagonism of interferon. Curr. Opin. Virol. 2, 264–275 (2012).

    Article  CAS  Google Scholar 

  8. Zampieri, C. A., Sullivan, N. J. & Nabel, G. J. Immunopathology of highly virulent pathogens: insights from Ebola virus. Nat. Immunol. 8, 1159–1164 (2007).

    Article  CAS  Google Scholar 

  9. Swanepoel, R. et al. Experimental inoculation of plants and animals with Ebola virus. Emerg. Infect. Dis. 2, 321–325 (1996).

    Article  CAS  Google Scholar 

  10. Watanabe, S. et al. Bat coronaviruses and experimental infection of bats, the Philippines. Emerg. Infect. Dis. 16, 1217–1223 (2010).

    Article  CAS  Google Scholar 

  11. Munster, V. J. et al. Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis). Sci. Rep. 6, 21878 (2016).

    Article  CAS  Google Scholar 

  12. Middleton, D. J. et al. Experimental Nipah virus infection in pteropid bats (Pteropus poliocephalus). J. Comp. Pathol. 136, 266–272 (2007).

    Article  CAS  Google Scholar 

  13. Olival, K. J. et al. Host and viral traits predict zoonotic spillover from mammals. Nature 546, 646–650 (2017).

    Article  CAS  Google Scholar 

  14. Wilkinson, G. S. & South, J. M. Life history, ecology and longevity in bats. Aging Cell 1, 124–131 (2002).

    Article  CAS  Google Scholar 

  15. Thomas, S. P. & Suthers, R. A. The physiology and energetics of bat flight. J. Exp. Biol. 57, 317–335 (1972).

    Google Scholar 

  16. Pavlovich, S. S. et al. The Egyptian rousette genome reveals unexpected features of bat antiviral immunity. Cell 173, 1098–1110 (2018).

    Article  CAS  Google Scholar 

  17. Zhang, G. et al. Comparative analysis of bat genomes provides insight into the evolution of flight and immunity. Science 339, 456–460 (2013).

    Article  CAS  Google Scholar 

  18. Glennon, N. B., Jabado, O., Lo, M. K. & Shaw, M. L. Transcriptome profiling of the virus-induced innate immune response in Pteropus vampyrus and its attenuation by Nipah virus interferon antagonist functions. J. Virol. 89, 7550–7566 (2015).

    Article  CAS  Google Scholar 

  19. Wynne, J. W. et al. Proteomics informed by transcriptomics reveals Hendra virus sensitizes bat cells to TRAIL-mediated apoptosis. Genome Biol. 15, 532 (2014).

    PubMed  PubMed Central  Google Scholar 

  20. Papenfuss, A. T. et al. The immune gene repertoire of an important viral reservoir, the Australian black flying fox. BMC Genomics 13, 261 (2012).

    Article  CAS  Google Scholar 

  21. Xie, J. et al. Dampened STING-dependent interferon activation in bats. Cell Host Microbe 23, 297–301 (2018).

    Article  CAS  Google Scholar 

  22. De La Cruz-Rivera, P. C. et al. The IFN response in bats displays distinctive IFN-stimulated gene expression kinetics with atypical RNASEL induction. J. Immunol. 200, 209–217 (2018).

    Article  Google Scholar 

  23. Zhou, P. et al. Contraction of the type I IFN locus and unusual constitutive expression of IFN-alpha in bats. Proc. Natl Acad. Sci. USA 113, 2696–2701 (2016).

    Article  CAS  Google Scholar 

  24. Shimada, K. et al. Oxidized mitochondrial DNA activates the NLRP3 inflammasome during apoptosis. Immunity 36, 401–414 (2012).

    Article  CAS  Google Scholar 

  25. Mariathasan, S. et al. Cryopyrin activates the inflammasome in response to toxins and ATP. Nature 440, 228–232 (2006).

    Article  CAS  Google Scholar 

  26. Iyer, S. S. et al. Mitochondrial cardiolipin is required for Nlrp3 inflammasome activation. Immunity 39, 311–323 (2013).

    Article  CAS  Google Scholar 

  27. Kuriakose, T. & Kanneganti, T. D. Regulation and functions of NLRP3 inflammasome during influenza virus infection. Mol. Immunol. 86, 56–64 (2017).

    Article  CAS  Google Scholar 

  28. Sha, W. et al. Human NLRP3 inflammasome senses multiple types of bacterial RNAs. Proc. Natl Acad. Sci. USA 111, 16059–16064 (2014).

    Article  CAS  Google Scholar 

  29. Youm, Y. H. et al. Canonical Nlrp3 inflammasome links systemic low-grade inflammation to functional decline in aging. Cell Metab. 18, 519–532 (2013).

    Article  CAS  Google Scholar 

  30. Guo, H., Callaway, J. B. & Ting, J. P. Inflammasomes: mechanism of action, role in disease, and therapeutics. Nat. Med. 21, 677–687 (2015).

    Article  Google Scholar 

  31. Lupfer, C., Malik, A. & Kanneganti, T. D. Inflammasome control of viral infection. Curr. Opin. Virol. 12, 38–46 (2015).

    Article  CAS  Google Scholar 

  32. Chakrabarti, A. et al. RNase L activates the NLRP3 inflammasome during viral infections. Cell Host Microbe 17, 466–477 (2015).

    Article  CAS  Google Scholar 

  33. Tong, S. et al. A distinct lineage of influenza A virus from bats. Proc. Natl Acad. Sci. USA 109, 4269–4274 (2012).

    Article  CAS  Google Scholar 

  34. Lawrence, T. M., Hudacek, A. W., de Zoete, M. R., Flavell, R. A. & Schnell, M. J. Rabies virus is recognized by the NLRP3 inflammasome and activates interleukin-1β release in murine dendritic cells. J. Virol. 87, 5848–5857 (2013).

    Article  CAS  Google Scholar 

  35. Johnson, N. et al. Human rabies due to lyssavirus infection of bat origin. Vet. Microbiol. 142, 151–159 (2010).

    Article  CAS  Google Scholar 

  36. Ren, R. et al. The H7N9 influenza A virus infection results in lethal inflammation in the mammalian host via the NLRP3-caspase-1 inflammasome. Sci. Rep. 7, 7625 (2017).

    Article  Google Scholar 

  37. Wang, W. et al. Zika virus infection induces host inflammatory responses by facilitating NLRP3 inflammasome assembly and interleukin-1β secretion. Nat. Commun. 9, 106 (2018).

    Article  Google Scholar 

  38. Coates, B. M. et al. Inhibition of the NOD-like receptor protein 3 inflammasome is protective in juvenile influenza A virus iInfection. Front. Immunol. 8, 782 (2017).

    Article  Google Scholar 

  39. Tate, M. D. et al. Reassessing the role of the NLRP3 inflammasome during pathogenic influenza A virus infection via temporal inhibition. Sci. Rep. 6, 27912 (2016).

    Article  CAS  Google Scholar 

  40. Lu, A. et al. Unified polymerization mechanism for the assembly of ASC-dependent inflammasomes. Cell 156, 1193–1206 (2014).

    Article  CAS  Google Scholar 

  41. LaRock, C. N. & Cookson, B. T. Burning down the house: cellular actions during pyroptosis. PLoS Pathog. 9, e1003793 (2013).

    Article  Google Scholar 

  42. Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S. & Coon, J. J. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics 11, 1475–1488 (2012).

    Article  Google Scholar 

  43. Bauernfeind, F. G. et al. Cutting edge: NF-κB activating pattern recognition and cytokine receptors license NLRP3 inflammasome activation by regulating NLRP3 expression. J. Immunol. 183, 787–791 (2009).

    Article  CAS  Google Scholar 

  44. O’Connor, W. Jr, Harton, J. A., Zhu, X., Linhoff, M. W. & Ting, J. P. Cutting edge: CIAS1/cryopyrin/PYPAF1/NALP3/CATERPILLER 1.1 is an inducible inflammatory mediator with NF-κB suppressive properties. J. Immunol. 171, 6329–6333 (2003).

    Article  Google Scholar 

  45. Chua, K. B. et al. A previously unknown reovirus of bat origin is associated with an acute respiratory disease in humans. Proc. Natl Acad. Sci. USA 104, 11424–11429 (2007).

    Article  CAS  Google Scholar 

  46. Hu, B., Ge, X., Wang, L. F. & Shi, Z. Bat origin of human coronaviruses. Virol. J. 12, 221 (2015).

    Article  Google Scholar 

  47. Peck, K. M. et al. Permissivity of dipeptidyl peptidase 4 orthologs to Middle East respiratory syndrome coronavirus is governed by glycosylation and other complex determinants. J. Virol. 91, e00534-17 (2017).

    Article  Google Scholar 

  48. Coll, R. C. et al. A small-molecule inhibitor of the NLRP3 inflammasome for the treatment of inflammatory diseases. Nat. Med. 21, 248–255 (2015).

    Article  CAS  Google Scholar 

  49. Zhou, P. et al. Unlocking bat immunology: establishment of Pteropus alecto bone marrow-derived dendritic cells and macrophages. Sci. Rep. 6, 38597 (2016).

    Article  CAS  Google Scholar 

  50. Netea, M. G., Wijmenga, C. & O’Neill, L. A. Genetic variation in Toll-like receptors and disease susceptibility. Nat. Immunol. 13, 535–542 (2012).

    Article  CAS  Google Scholar 

  51. Werling, D., Jann, O. C., Offord, V., Glass, E. J. & Coffey, T. J. Variation matters: TLR structure and species-specific pathogen recognition. Trends Immunol. 30, 124–130 (2009).

    Article  CAS  Google Scholar 

  52. Py, B. F., Kim, M. S., Vakifahmetoglu-Norberg, H. & Yuan, J. Deubiquitination of NLRP3 by BRCC3 critically regulates inflammasome activity. Mol. Cell 49, 331–338 (2013).

    Article  CAS  Google Scholar 

  53. Mitoma, H. et al. The DHX33 RNA helicase senses cytosolic RNA and activates the NLRP3 inflammasome. Immunity 39, 123–135 (2013).

    Article  CAS  Google Scholar 

  54. Surya, W., Li, Y., Verdia-Baguena, C., Aguilella, V. M. & Torres, J. MERS coronavirus envelope protein has a single transmembrane domain that forms pentameric ion channels. Virus Res. 201, 61–66 (2015).

    Article  CAS  Google Scholar 

  55. O’Shea, T. J. et al. Bat flight and zoonotic viruses. Emerg. Infect. Dis. 20, 741–745 (2014).

    Article  Google Scholar 

  56. Schountz, T., Baker, M. L., Butler, J. & Munster, V. Immunological control of viral infections in bats and the emergence of viruses highly pathogenic to humans. Front. Immunol. 8, 1098 (2017).

    Article  Google Scholar 

  57. Miller, M. R. et al. Broad and temperature independent replication potential of filoviruses on cells derived from old and new world bat species. J. Infect. Dis. 214, S297–S302 (2016).

    Article  CAS  Google Scholar 

  58. Ying, T. et al. Exceptionally potent neutralization of Middle East respiratory syndrome coronavirus by human monoclonal antibodies. J. Virol. 88, 7796–7805 (2014).

    Article  Google Scholar 

  59. Crameri, G. et al. Establishment, immortalisation and characterisation of pteropid bat cell lines. PLoS One 4, e8266 (2009).

    Article  Google Scholar 

  60. Ahn, J., Gutman, D., Saijo, S. & Barber, G. N. STING manifests self DNA-dependent inflammatory disease. Proc. Natl Acad. Sci. USA 109, 19386–19391 (2012).

    Article  CAS  Google Scholar 

  61. Li, Y. et al. Host range, prevalence, and genetic diversity of adenoviruses in bats. J. Virol. 84, 3889–3897 (2010).

    Article  CAS  Google Scholar 

  62. Hornung, V. et al. Silica crystals and aluminum salts activate the NALP3 inflammasome through phagosomal destabilization. Nat. Immunol. 9, 847–856 (2008).

    Article  CAS  Google Scholar 

  63. Sadler, A. J., Latchoumanin, O., Hawkes, D., Mak, J. & Williams, B. R. An antiviral response directed by PKR phosphorylation of the RNA helicase A. PLoS Pathog. 5, e1000311 (2009).

    Article  Google Scholar 

  64. Trapnell, C. et al. Differential gene and transcript expression analysis of RNA–seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578 (2012).

    Article  CAS  Google Scholar 

  65. Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).

    Article  CAS  Google Scholar 

  66. MacLean, B. et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966–968 (2010).

    Article  CAS  Google Scholar 

  67. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was funded by the Singapore National Research Foundation (grants NRF2012NRF-CRP001–056 to F.G. and L.-F.W. and NRF2016NRF-NSFC002–013 to L.-F.W.), a New Investigator’s Grant (to A.T.I.) from the National Medical Research Council of Singapore (NMRC/BNIG/2040/2015) and the National Natural Science Foundation of China (31621061). R.M.S. is supported by a Young Investigator Grant YIG 2015 (BMRC, A*STAR) and NMRC MS-CETSA platform grant (MOHIAFCAT2/004/2015). The authors thank the following for help with bat sampling: Crameri Research Consulting, J. Meers, H. Field and Duke-NUS team members (for a detailed listing see Supplementary Information). The authors thank A. Bertoletti and A. T. Tan for use of the Amnis ImageStream. The authors give special thanks to E. Latz for providing the immortalized NLRP3-knockout macrophages. The authors also acknowledge the facilities and technical assistance of the Advanced Bioimaging Core and Flow Cytometry Core at SingHealth Duke-NUS Academic Medical Centre, and X. F. Lim and S. Velraj for their valuable assistance in the Duke-NUS ABSL3 Facility.

Author information

Authors and Affiliations

Authors

Contributions

M.A., A.T.I. and L.-F.W. conceived the study. J.H.J.N., Z.-L.S. and L.-F.W. provided resources and materials. M.A., D.E.A., Q.Z., C.W.T., B.L.L., W.N.C., S.M., R.M.S., K.L. and A.T.I. performed experiments. M.A., D.E.A., Q.Z., C.W.T., R.M.S., W.M., L.C.W. and A.T.I. performed analysis. C.A.D and F.G. provided access to splenocyte subset RNA–seq data. M.A., A.T.I. and L.-F.W. wrote the manuscript with input from all authors. Correspondence and requests for materials should be addressed to A.T.I. and L.-F.W.

Corresponding authors

Correspondence to Aaron T. Irving or Lin-Fa Wang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ahn, M., Anderson, D.E., Zhang, Q. et al. Dampened NLRP3-mediated inflammation in bats and implications for a special viral reservoir host. Nat Microbiol 4, 789–799 (2019). https://doi.org/10.1038/s41564-019-0371-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41564-019-0371-3

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing