Interferon-inducible cytoplasmic lncLrrc55-AS promotes antiviral innate responses by strengthening IRF3 phosphorylation

Abstract

Type I interferon (IFN-I) production is efficiently induced to ensure a potent innate immune response to viral infection. How this response can be enhanced, however, remains to be explored. Here, we identify a new cytoplasmic long non-coding RNA (lncRNA), lncLrrc55-AS, that drives a positive feedback loop to promote interferon regulatory factor 3 (IRF3) signaling and IFN-I production. We show that lncLrrc55-AS is virus-induced in multiple cell types via the IFN-JAK-STAT pathway. LncLrrc55-AS-deficient mice display a weakened antiviral immune response and are more susceptible to viral challenge. Mechanistically, lncLrrc55-AS binds phosphatase methylesterase 1 (PME-1), and promotes the interaction between PME-1 and the phosphatase PP2A, an inhibitor of IRF3 signaling. LncLrrc55-AS supports PME-1-mediated demethylation and inactivation of PP2A, thereby enhancing IRF3 phosphorylation and signaling. Loss of PME-1 phenocopies lncLrrc55-AS deficiency, leading to diminished IRF3 phosphorylation and IFN-I production. We have identified an IFN-induced lncRNA as a positive regulator of IFN-I production, adding mechanistic insight into lncRNA-mediated regulation of signaling in innate immunity and inflammation.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

References

  1. 1.

    McNab, F. et al. Type I interferons in infectious disease. Nat. Rev. Immunol. 15, 87–103 (2015).

  2. 2.

    Hoffmann, H. H., Schneider, W. M. & Rice, C. M. Interferons and viruses: an evolutionary arms race of molecular interactions. Trends Immunol. 36, 124–138 (2015).

  3. 3.

    Wu, J. & Chen, Z. J. Innate immune sensing and signaling of cytosolic nucleic acids. Annu. Rev. Immunol. 32, 461–488 (2014).

  4. 4.

    Liu, S. et al. Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation. Science 347, aaa2630 (2015).

  5. 5.

    Liu, J., Qian, C. & Cao, X. Post-translational modification control of innate immunity. Immunity 45, 15–30 (2016).

  6. 6.

    Fitzgerald, K. A. et al. IKKε and TBK1 are essential components of the IRF3 signaling pathway. Nat. Immunol. 4, 491–496 (2003).

  7. 7.

    Long, L. et al. Recruitment of phosphatase PP2A by RACK1 adaptor protein deactivates transcription factor IRF3 and limits type I interferon signaling. Immunity 40, 515–529 (2014).

  8. 8.

    Shen, Q. et al. Tet2 promotes pathogen infection-induced myelopoiesis through mRNA oxidation. Nature 554, 123–127 (2018).

  9. 9.

    Schlums, H. et al. Cytomegalovirus infection drives adaptive epigenetic diversification of NK cells with altered signaling and effector function. Immunity 42, 443–456 (2015).

  10. 10.

    Chiappinelli, K. B. et al. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. Cell 162, 974–986 (2015).

  11. 11.

    Marazzi, I., Greenbaum, B. D., Low, D. H. P. & Guccione, E. Chromatin dependencies in cancer and inflammation. Nat. Rev. Mol. Cell Biol. 19, 245–261 (2018).

  12. 12.

    Chen, Y. G., Satpathy, A. T. & Chang, H. Y. Gene regulation in the immune system by long noncoding RNAs. Nat. Immunol. 18, 962–972 (2017).

  13. 13.

    Atianand, M. K. et al. A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation. Cell 165, 1672–1685 (2016).

  14. 14.

    Liu, B. et al. Long noncoding RNA lncKdm2b is required for ILC3 maintenance by initiation of Zfp292 expression. Nat. Immunol. 18, 499–508 (2017).

  15. 15.

    Morchikh, M. et al. HEXIM1 and NEAT1 Long non-coding RNA form a multi-subunit complex that regulates DNA-mediated innate immune response. Mol. Cell 67, 387–399 (2017).

  16. 16.

    Nishitsuji, H. et al. Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression. Proc. Natl Acad. Sci. USA 113, 10388–10393 (2016).

  17. 17.

    Wang, P., Xu, J., Wang, Y. & Cao, X. An interferon-independent lncRNA promotes viral replication by modulating cellular metabolism. Science 358, 1051–1055 (2017).

  18. 18.

    Xie, Q. et al. Long noncoding RNA ITPRIP-1 positively regulates the innate immune response through promotion of oligomerization and activation of MDA5. J. Virol. 92, e00507–e00518 (2018).

  19. 19.

    Winterling, C. et al. Evidence for a crucial role of a host non-coding RNA in influenza A virus replication. RNA Biol. 11, 66–75 (2014).

  20. 20.

    Jiang, M. et al. Self-recognition of an inducible host lncRNA by RIG-I feedback restricts innate immune response. Cell 173, 906–919 (2018).

  21. 21.

    Carnero, E. et al. Long noncoding RNA EGOT negatively affects the antiviral response and favors HCV replication. EMBO Rep. 17, 1013–1028 (2016).

  22. 22.

    Chu, C., Qu, K., Zhong, F. L., Artandi, S. E. & Chang, H. Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 44, 667–678 (2011).

  23. 23.

    Longin, S. et al. Spatial control of protein phosphatase 2A (de)methylation. Exp. Cell Res. 314, 68–81 (2008).

  24. 24.

    Xing, Y. et al. Structural mechanism of demethylation and inactivation of protein phosphatase 2A. Cell 133, 154–163 (2008).

  25. 25.

    Peng, D. et al. A novel function of F-Box protein FBXO17 in negative regulation of type I IFN signaling by recruiting PP2A for IFN regulatory factor 3 deactivation. J. Immunol. 198, 808–819 (2017).

  26. 26.

    Kaur, A. & Westermarck, J. Regulation of protein phosphatase 2A (PP2A) tumor suppressor function by PME-1. Biochem. Soc. Trans. 44, 1683–1693 (2016).

  27. 27.

    Albano, C. et al. The total activity of a mixture of okadaic acid-group compounds can be calculated by those of individual analogues in a phosphoprotein phosphatase 2A assay. Toxicon 53, 631–637 (2009).

  28. 28.

    Meng, G. et al. Combination treatment with triptolide and hydroxycamptothecin synergistically enhances apoptosis in A549 lung adenocarcinoma cells through PP2A-regulated ERK, p38 MAPKs and Akt signaling pathways. Int. J. Oncol. 46, 1007–1017 (2015).

  29. 29.

    Ivaska, J., Bosca, L. & Parker, P. J. PKCε is a permissive link in integrin-dependent IFN-γ signalling that facilitates JAK phosphorylation of STAT1. Nat. Cell Biol. 5, 363–369 (2003).

  30. 30.

    Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26–46 (2013).

  31. 31.

    Munschauer, M. et al. The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. Nature 561, 132–136 (2018).

  32. 32.

    Satpathy, A. T. & Chang, H. Y. Long noncoding RNA in hematopoiesis and immunity. Immunity 42, 792–804 (2015).

  33. 33.

    Schneider, W. M., Chevillotte, M. D. & Rice, C. M. Interferon-stimulated genes: a complex web of host defenses. Annu. Rev. Immunol. 32, 513–545 (2014).

  34. 34.

    Carnero, E. et al. Type I interferon regulates the expression of long non-coding RNAs. Front. Immunol. 5, 548 (2014).

  35. 35.

    Carpenter, S. et al. A long noncoding RNA mediates both activation and repression of immune response genes. Science 341, 789–792 (2013).

  36. 36.

    Imamura, K. et al. Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. Mol. Cell 53, 393–406 (2014).

  37. 37.

    Ma, H. et al. The Long noncoding RNA NEAT1 exerts antihantaviral effects by acting as positive feedback for RIG-I signaling. J. Virol. 91, e02250–16 (2017).

  38. 38.

    Gough, D. J. et al. Constitutive type I interferon modulates homeostatic balance through tonic signaling. Immunity 36, 166–174 (2012).

  39. 39.

    Yang, F., Zhang, H., Mei, Y. & Wu, M. Reciprocal regulation of HIF-1α and lincRNA-p21 modulates the Warburg effect. Mol. Cell 53, 88–100 (2014).

  40. 40.

    Rapicavoli, N. A. et al. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. Elife 2, e00762 (2013).

  41. 41.

    Liu, B. et al. A cytoplasmic NF-κB interacting long noncoding RNA blocks IκB phosphorylation and suppresses breast cancer metastasis. Cancer Cell 27, 370–381 (2015).

  42. 42.

    Chattopadhyay, S. et al. Inhibition of viral pathogenesis and promotion of the septic shock response to bacterial infection by IRF-3 are regulated by the acetylation and phosphorylation of its coactivators. mBio 4, e00636–00612 (2013).

  43. 43.

    Yu, Y. & Hayward, G. S. The ubiquitin E3 ligase RAUL negatively regulates type I interferon through ubiquitination of the transcription factors IRF7 and IRF3. Immunity 33, 863–877 (2010).

  44. 44.

    Atianand, M. K., Caffrey, D. R. & Fitzgerald, K. A. Immunobiology of long noncoding RNAs. Annu. Rev. Immunol. 35, 177–198 (2017).

  45. 45.

    Nakagawa, S. & Kageyama, Y. Nuclear lncRNAs as epigenetic regulators-beyond skepticism. Biochim. Biophys. Acta 1839, 215–222 (2014).

  46. 46.

    Hentze, M. W., Castello, A., Schwarzl, T. & Preiss, T. A brave new world of RNA-binding proteins. Nat. Rev. Mol. Cell Biol. 19, 327–341 (2018).

  47. 47.

    Wang, K. C. & Chang, H. Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904–914 (2011).

  48. 48.

    Cao, X. Self-regulation and cross-regulation of pattern-recognition receptor signalling in health and disease. Nat. Rev. Immunol. 16, 35–50 (2016).

  49. 49.

    Dhayalan, A. et al. The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J. Biol. Chem. 285, 26114–26120 (2010).

Download references

Acknowledgements

We thank Dr. Pin Wang for technical assistance. This work is supported by grants from the National Natural Science Foundation of China (81788101 to X.C.), the National Key Research & Development Program of China (2018YFA0507403 to X.C.), and CAMS Innovation Fund for Medical Sciences (2016-12M-1-003 to X.C.).

Author information

X.C. designed and supervised the research; Y.Z., M.L., Y.X., Z.L., W.W. and X.L. performed the experiments; Y.M. and L.Z. generated KO mice; Z.S. provided reagents; X.C. and Y.Z. analyzed the data and wrote the manuscript.

Correspondence to Xuetao Cao.

Ethics declarations

Competing interests

The authors declare no competing interests.

Supplementary information

Supplementary information, Figure S1

Supplementary information, Figure S2

Supplementary informaiton, Figure S3

Supplementary information, Figure S4

Supplementary information, Figure S5

Supplementary information, Figure S6

Supplementary information, Figure S7

Supplementary information, Figure S8

Supplementary information, Figure S9

Supplementary information, Figure S10

Supplementary information, Table S1

Supplementary information, Table S2

Supplementary information, Table S3

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark