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:

CRISPR/Cas9-mediated deletion of miR-146a enhances antiviral response in HIV-1 infected cells

Genes & Immunity volume 20, pages 327–337 (2019)Cite this article

Subjects

Abstract

The human immunodeficiency virus type 1 (HIV-1) causes persistent infection in human and induces miR-146a expression in infected cells. miR-146a represses the innate immune response by inhibiting the expression of TRAF6 and IRAK1 genes, thus negatively controls the NF-κB-related cytokines and interferon stimulated genes. Here we reported that lentiviral CRISPR/Cas9 system was highly efficient in introducing mutations in the precursor miR-146a genomic sequences, resulting in a loss of miR-146a expression and function. miR-146a ablation led to increasing cytokines production in LPS-stimulated A549 cells. Moreover, miR-146a knockout in HIV-1 infected MT2 cells markedly increased the expression of cytokines and HIV-1 restriction factors and reversed T cell exhaustion markers expression, thus influencing HIV-1 replication. Our study indicates that lentiviral CRISPR/Cas9-mediated gene editing is an effective approach to abrogate miR-146a expression, which consequently inhibits HIV-1 replication as well as proviral reactivation by enhancing the expression of cytokines and HIV-1 restriction factors.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Dong CS, Qu L, Wang HY, Wei L, Dong YS, Xiong SD. Targeting hepatitis B virus cccDNA by CRISPR/Cas9 nuclease efficiently inhibits viral replication. Antivir Res. 2015;118:110–17.

    Article  CAS  Google Scholar 

  2. van Diemen FR, Kruse EM, Hooykaas MJG, Bruggeling CE, Schurch AC, van Ham PM, et al. CRISPR/Cas9-mediated genome editing of herpesviruses limits productive and latent infections. Plos Pathogens. 2016;12:e1005701.

    Article  Google Scholar 

  3. Kaminski R, Chen Y, Fischer T, Tedaldi E, Napoli A, Zhang Y, et al. Elimination of HIV-1 genomes from human T-lymphoid cells by CRISPR/Cas9 gene editing. Sci Rep. 2016;6:22555.

    Article  CAS  Google Scholar 

  4. Wang Q, Chen S, Xiao Q, Liu Z, Liu S, Hou P, et al. Genome modification of CXCR4 by Staphylococcus aureus Cas9 renders cells resistance to HIV-1 infection. Retrovirology. 2017;14:51.

    Article  Google Scholar 

  5. Li C, Guan XM, Du T, Jin W, Wu B, Liu YL, et al. Inhibition of HIV-1 infection of primary CD4(+) T-cells by gene editing of CCR5 using adenovirus-delivered CRISPR/Cas9. J General Virol. 2015;96:2381–93.

    Article  CAS  Google Scholar 

  6. Nguyen EV, Gharib SA, Crothers K, Chow YH, Park DR, Goodlett DR, et al. Proteomic landscape of bronchoalveolar lavage fluid in human immunodeficiency virus infection. Am J Physiol-Lung Cell Mol Physiol. 2014;306:L35–L42.

    Article  CAS  Google Scholar 

  7. Foldi J, Kozhaya L, McCarty B, Mwamzuka M, Marshed F, Ilmet T, et al. HIV-infected children have elevated levels of PD-1(+) memory CD4 T cells with low proliferative capacity and high inflammatory cytokine effector functions. J Infect Dis. 2017;216:641–50.

    Article  CAS  Google Scholar 

  8. Trautmann L, Janbazian L, Chomont N, Said EA, Gimmig S, Bessette B, et al. Upregulation of PD-1 expression on HIV-specific CD8(+) T cells leads to reversible immune dysfunction. Nat Med. 2006;12:1198–202.

    Article  CAS  Google Scholar 

  9. Velu V, Shetty RD, Larsson M, Shankar EM. Role of PD-1 co-inhibitory pathway in HIV infection and potential therapeutic options. Retrovirology. 2015;12:14.

    Article  Google Scholar 

  10. Hunt PW. HIV and inflammation: mechanisms and consequences. Curr HIV/AIDS Rep. 2012;9:139–47.

    Article  Google Scholar 

  11. Stacey AR, Norris PJ, Qin L, Haygreen EA, Taylor E, Heitman J, et al. Induction of a striking systemic cytokine cascade prior to peak viremia in acute human immunodeficiency virus type 1 infection, in contrast to more modest and delayed responses in acute hepatitis B and C virus infections. J Virol. 2009;83:3719–33.

    Article  CAS  Google Scholar 

  12. Zhao GX, Liu LF, Su B, Zhang T, Chen P, Li W, et al. The dynamic changes of interferon lambdas relatedgenes and proteins in JAK/STAT pathway in both acute and chronic HIV-1 infected patients. AIDS Res Therapy. 2017;14:31.

    Article  Google Scholar 

  13. Honda K, Takaoka A, Taniguchi T. Type I inteferon gene induction by the interferon regulatory factor family of transcription factors. Immunity. 2006;25:349–60.

    Article  CAS  Google Scholar 

  14. Anderson P. Post-transcriptional control of cytokine production. Nat Immunol. 2008;9:353–9.

    Article  CAS  Google Scholar 

  15. Savan R. Post-transcriptional regulation of interferons and their signaling pathways. J Interferon Cytokine Res. 2014;34:318–29.

    Article  CAS  Google Scholar 

  16. Taganov KD, Boldin MP, Chang KJ, Baltimore D. NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci USA. 2006;103:12481–6.

    Article  CAS  Google Scholar 

  17. Perry MM, Moschos SA, Williams AE, Shepherd NJ, Larner-Svensson HM, Lindsay MA. Rapid changes in microRNA-146a expression negatively regulate the IL-1beta-induced inflammatory response in human lung alveolar epithelial cells. J Immunol. 2008;180:5689–98.

    Article  CAS  Google Scholar 

  18. Wang S, Zhang X, Ju Y, Zhao B, Yan X, Hu J, et al. MicroRNA-146a feedback suppresses T cell immune function by targeting Stat1 in patients with chronic hepatitis B. J Immunol. 2013;191:293–301.

    Article  CAS  Google Scholar 

  19. Hou Z, Zhang J, Han Q, Su C, Qu J, Xu D, et al. Hepatitis B virus inhibits intrinsic RIG-I and RIG-G immune signaling via inducing miR146a. Sci Rep. 2016;6:26150.

    Article  CAS  Google Scholar 

  20. Duskova K, Nagilla P, Le HS, Iyer P, Thalamuthu A, Martinson J, et al. MicroRNA regulation and its effects on cellular transcriptome in Human Immunodeficiency Virus-1 (HIV-1) infected individuals with distinct viral loadand CD4 cell counts. BMC Infectious Dis. 2013;13:250.

  21. Rom S, Rom I, Passiatore G, Pacifici M, Radhakrishnan S, Del Valle L, et al. CCL8/MCP-2 is a target for mir-146a in HIV-1-infected human microglial cells. FASEB J.2010;24:2292–300.

    Article  CAS  Google Scholar 

  22. Egana-Gorrono L, Escriba T, Boulanger N, Guardo AC, Leon A, Bargallo ME, et al. Differential MicroRNA expression profile between stimulated PBMCs from HIV-1 infected elite controllers and viremic progressors. PLoS ONE. 2014;9:e106360.

    Article  Google Scholar 

  23. Feng Y, Zhang XX, Song QF, Li TB, Zeng Y. Drosha processing controls the specificity and efficiency of global microRNA expression. Biochim Et Biophys Acta-Gene Regul Mech. 2011;1809:700–7.

    Article  CAS  Google Scholar 

  24. Feng Y, Zhang XX, Graves P, Zeng Y. A comprehensive analysis of precursor microRNA cleavage by human Dicer. Rna-a Publ Rna Soc. 2012;18:2083–92.

    Article  CAS  Google Scholar 

  25. Qu XY, Wang PF, Ding DL, Li L, Wang HB, Ma L, et al. Zinc-finger-nucleases mediate specific and efficient excision of HIV-1 proviral DNA from infected and latently infected human T cells. Nucleic Acids Res. 2013;41:7771–82.

    Article  CAS  Google Scholar 

  26. D’Elia RV, Harrison K, Oyston PC, Lukaszewski RA, Clark GC. Targeting the “cytokine storm” for therapeutic benefit. Clin Vaccin Immunol. 2013;20:319–27.

    Article  Google Scholar 

  27. Chousterman BG, Swirski FK, Weber GF. Cytokine storm and sepsis disease pathogenesis. Semin Immunopathol. 2017;39:517–28.

    Article  CAS  Google Scholar 

  28. Tisoncik JR, Korth MJ, Simmons CP, Farrar J, Martin TR, Katze MG. Into the eye of the cytokine storm. Microbiol Mol Biol Rev. 2012;76:16–32.

    Article  CAS  Google Scholar 

  29. Kassu A, Marcus RA, D’Souza MB, Kelly-McKnight EA, Golden-Mason L, Akkina R, et al. Regulation of virus-specific CD4(+) T cell function by multiple costimulatory receptors during chronic HIV infection. J Immunol. 2010;185:3007–18.

    Article  CAS  Google Scholar 

  30. Kaufmann DE, Kavanagh DG, Pereyra F, Zaunders JJ, Mackey EW, Miura T, et al. Upregulation of CTLA-4 by HIV-specific CD4+ T cells correlates with disease progression and defines a reversible immune dysfunction. Nat Immunol. 2007;8:1246–54.

    Article  CAS  Google Scholar 

  31. Sun T, Li X, Song H, Gao F, Zhou G, Li X, et al. MiR-146a aggravates LPS-induced inflammatory injury by targeting CXCR4 in the articular chondrocytes. Cell Physiol Biochem. 2017;44:1282–94.

    Article  CAS  Google Scholar 

  32. Chen QZ, Luo F, Lu MX, Li N, Teng Y, Huang QL, et al. HTNV-induced upregulation of miR-146a in HUVECs promotes viral infection by modulating pro-inflammatory cytokine release. Biochem Biophys Res Commun. 2017;493:807–13.

    Article  CAS  Google Scholar 

  33. Fu Y, Zhang L, Zhang F, Tang T, Zhou Q, Feng C, et al. Exosome-mediated miR-146a transfer suppresses type I interferon response and facilitates EV71 infection. PLoS Pathog. 2017;13:e1006611.

    Article  Google Scholar 

  34. Deng SM, Wang HL, Jia CL, Zhu SK, Chu XM, Ma Q, et al. MicroRNA-146a induces lineage-negative bone marrow cell apoptosis and senescence by targeting polo-like kinase 2 expression. Arterioscler Thromb Vasc Biol. 2017;37:280.

    Article  CAS  Google Scholar 

  35. Angelini F, Pagano F, Bordin A, Picchio V, De Falco E, Chimenti I. Getting old through the blood: circulating molecules in aging and senescence of cardiovascular regenerative cells. Front Cardiovasc Med. 2017;4:62.

    Article  Google Scholar 

  36. Olivieri F, Lazzarini R, Recchioni R, Marcheselli F, Rippo MR, Di Nuzzo S, et al. MiR-146a as marker of senescence-associated pro-inflammatory status in cells involved in vascular remodelling. Age. 2013;35:1157–72.

    Article  CAS  Google Scholar 

  37. Li D, Duan MY, Feng Y, Geng LL, Li XQ, Zhang WG. MiR-146a modulates macrophage polarization in systemic juvenile idiopathic arthritis by targeting INHBA. Mol Immunol. 2016;77:205–12.

    Article  CAS  Google Scholar 

  38. Huang C, Liu XJ, QunZhou, Xie J, Ma TT, Meng XM, et al. MiR-146a modulates macrophage polarization by inhibiting Notch1 pathway in RAW264.7 macrophages. Int Immunopharmacol. 2016;32:46–54.

    Article  Google Scholar 

  39. Fu YF, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol. 2014;32:279–84.

    Article  CAS  Google Scholar 

  40. Li L, Feng HM, Da Q, Jiang HL, Chen L, Xie LL, et al. Expression of HIV-encoded microRNA-TAR and its inhibitory effect on viral replication in human primary macrophages. Arch Virol. 2016;161:1115–23.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research was supported by research grants from the National Natural Science Foundation of China (Nos. 81271818 and 81471940), project of Hubei Provincial Science & Technology (2015CFB184) to Y.F. And we appreciate Research grants from the National Natural Science Foundation of China (No. 81471941), the Science and Technology Ministry of China as part of a major project of infectious disease control and prevention carried out by W.H. (2014ZX10001003).

Author information

Author notes

  1. These authors contributed equally: Yan Teng and Mingqi Luo

Authors and Affiliations

  1. State Key Laboratory of Virology/Institute of Medical Virology/Hubei Province Key Laboratory of Allergy & Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, People’s Republic of China

    Yan Teng, Ting Yu, Lang Chen, Qiuling Huang, Shuliang Chen, Linlin Xie, Fan Luo, Hairong Xiong, Yuanyuan Liu, Wei Hou & Yong Feng

  2. Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, People’s Republic of China

    Mingqi Luo & Yong Feng

  3. Department of Zoology, College of Life Sciences, Nanjing Agriculture University, Nanjing, 210095, Jiangsu, People’s Republic of China

    Yan Zeng

Authors
  1. Yan Teng
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mingqi Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ting Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qiuling Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Shuliang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Linlin Xie
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yan Zeng
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Fan Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Hairong Xiong
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Yuanyuan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Wei Hou
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Yong Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Wei Hou or Yong Feng.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Teng, Y., Luo, M., Yu, T. et al. CRISPR/Cas9-mediated deletion of miR-146a enhances antiviral response in HIV-1 infected cells. Genes Immun 20, 327–337 (2019). https://doi.org/10.1038/s41435-018-0036-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41435-018-0036-x

This article is cited by

Search

Advanced search

Quick links