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Human cytomegalovirus microRNA miR-US4-1 inhibits CD8+ T cell responses by targeting the aminopeptidase ERAP1

Abstract

Major histocompatibility complex (MHC) class I molecules present peptides on the cell surface to CD8+ T cells, which is critical for the killing of virus-infected or transformed cells. Precursors of MHC class I–presented peptides are trimmed to mature epitopes by the aminopeptidase ERAP1. The US2–US11 genomic region of human cytomegalovirus (HCMV) is dispensable for viral replication and encodes three microRNAs (miRNAs). We show here that HCMV miR-US4-1 specifically downregulated ERAP1 expression during viral infection. Accordingly, the trimming of HCMV-derived peptides was inhibited, which led to less susceptibility of infected cells to HCMV-specific cytotoxic T lymphocytes (CTLs). Our findings identify a previously unknown viral miRNA–based CTL-evasion mechanism that targets a key step in the MHC class I antigen-processing pathway.

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Figure 1: Expression of HCMV miR-US4-1 results in less ERAP1b mRNA and protein but not less ERAP1a mRNA or protein.
Figure 2: HCMV miR-US4-1 targets the 3′ UTR of ERAP1b and physically binds to ERAP1b mRNA in the RISC.
Figure 3: Downregulation of ERAP1 in HCMV-infected HFF cells.
Figure 4: HCMV miR-US4 inhibits the trimming of OVA8 peptide from OVA precursor peptide by ERAP1.
Figure 5: HCMV miR-US4-1 inhibits the generation of HCMV-derived antigenic peptides and CD8+ CTL responses.

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References

  1. Hansen, T.H. & Bouvier, M. MHC class I antigen presentation: learning from viral evasion strategies. Nat. Rev. Immunol. 9, 503–513 (2009).

    Article  CAS  Google Scholar 

  2. Vyas, J.M., Van der Veen, A.G. & Ploegh, H.L. The known unknowns of antigen processing and presentation. Nat. Rev. Immunol. 8, 607–618 (2008).

    Article  CAS  Google Scholar 

  3. Nguyen, T.T. et al. Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1. Nat. Struct. Mol. Biol. 18, 604–613 (2011).

    Article  CAS  Google Scholar 

  4. Haroon, N. & Inman, R.D. Endoplasmic reticulum aminopeptidases: Biology and pathogenic potential. Nat. Rev. Rheumatol. 6, 461–467 (2010).

    Article  CAS  Google Scholar 

  5. Saric, T. et al. An IFN-γ-induced aminopeptidase in the ER, ERAP1, trims precursors to MHC class I–presented peptides. Nat. Immunol. 3, 1169–1176 (2002).

    Article  CAS  Google Scholar 

  6. Saveanu, L. et al. Concerted peptide trimming by human ERAP1 and ERAP2 aminopeptidase complexes in the endoplasmic reticulum. Nat. Immunol. 6, 689–697 (2005).

    Article  CAS  Google Scholar 

  7. Kanaseki, T. & Shastri, N. Endoplasmic reticulum aminopeptidase associated with antigen processing regulates quality of processed peptides presented by MHC class I molecules. J. Immunol. 181, 6275–6282 (2008).

    Article  CAS  Google Scholar 

  8. Hammer, G.E., Gonzalez, F., James, E., Nolla, H. & Shastri, N. In the absence of aminopeptidase ERAAP, MHC class I molecules present many unstable and highly immunogenic peptides. Nat. Immunol. 8, 101–108 (2007).

    Article  CAS  Google Scholar 

  9. Chang, S.C., Momburg, F., Bhutani, N. & Goldberg, A.L. The ER aminopeptidase, ERAP1, trims precursors to lengths of MHC class I peptides by a “molecular ruler” mechanism. Proc. Natl. Acad. Sci. USA 102, 17107–17112 (2005).

    Article  CAS  Google Scholar 

  10. Fabian, M.R., Sonenberg, N. & Filipowicz, W. Regulation of mRNA translation and stability by microRNAs. Annu. Rev. Biochem. 79, 351–379 (2010).

    Article  CAS  Google Scholar 

  11. Pfeffer, S. et al. Identification of virus-encoded microRNAs. Science 304, 734–736 (2004).

    Article  CAS  Google Scholar 

  12. Cullen, B.R. Viral and cellular messenger RNA targets of viral microRNAs. Nature 457, 421–425 (2009).

    Article  CAS  Google Scholar 

  13. Pfeffer, S. et al. Identification of microRNAs of the herpesvirus family. Nat. Methods 2, 269–276 (2005).

    Article  CAS  Google Scholar 

  14. Grey, F. et al. Identification and characterization of human cytomegalovirus-encoded microRNAs. J. Virol. 79, 12095–12099 (2005).

    Article  CAS  Google Scholar 

  15. Grey, F., Meyers, H., White, E.A., Spector, D.H. & Nelson, J. A human cytomegalovirus-encoded microRNA regulates expression of multiple viral genes involved in replication. PLoS Pathog. 3, e163 (2007).

    Article  Google Scholar 

  16. Grey, F. et al. A viral microRNA down-regulates multiple cell cycle genes through mRNA 5′UTRs. PLoS Pathog. 6, e1000967 (2010).

    Article  Google Scholar 

  17. Stern-Ginossar, N. et al. Host immune system gene targeting by a viral miRNA. Science 317, 376–381 (2007).

    Article  CAS  Google Scholar 

  18. Stern-Ginossar, N. et al. Analysis of human cytomegalovirus-encoded microRNA activity during infection. J. Virol. 83, 10684–10693 (2009).

    Article  CAS  Google Scholar 

  19. Rehm, A. et al. Human cytomegalovirus gene products US2 and US11 differ in their ability to attack major histocompatibility class I heavy chains in dendritic cells. J. Virol. 76, 5043–5050 (2002).

    Article  CAS  Google Scholar 

  20. Machold, R.P., Wiertz, E.J., Jones, T.R. & Ploegh, H.L. The HCMV gene products US11 and US2 differ in their ability to attack allelic forms of murine major histocompatibility complex (MHC) class I heavy chains. J. Exp. Med. 185, 363–366 (1997).

    Article  CAS  Google Scholar 

  21. Gruhler, A., Peterson, P.A. & Fruh, K. Human cytomegalovirus immediate early glycoprotein US3 retains MHC class I molecules by transient association. Traffic 1, 318–325 (2000).

    Article  CAS  Google Scholar 

  22. Lehner, P.J., Karttunen, J.T., Wilkinson, G.W. & Cresswell, P. The human cytomegalovirus US6 glycoprotein inhibits transporter associated with antigen processing-dependent peptide translocation. Proc. Natl. Acad. Sci. USA 94, 6904–6909 (1997).

    Article  CAS  Google Scholar 

  23. Park, B., Spooner, E., Houser, B.L., Strominger, J.L. & Ploegh, H.L. The HCMV membrane glycoprotein US10 selectively targets HLA-G for degradation. J. Exp. Med. 207, 2033–2041 (2010).

    Article  CAS  Google Scholar 

  24. Gustems, M. et al. Regulation of the transcription and replication cycle of human cytomegalovirus is insensitive to genetic elimination of the cognate NF-kappa B binding sites in the enhancer. J. Virol. 80, 9899–9904 (2006).

    Article  CAS  Google Scholar 

  25. Wu, J., O'Neill, J. & Barbosa, M.S. Transcription factor Sp1 mediates cell-specific trans-activation of the human cytomegalovirus DNA polymerase gene promoter by immediate-early protein IE86 in glioblastoma U373MG cells. J. Virol. 72, 236–244 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Chekulaeva, M. & Filipowicz, W. Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells. Curr. Opin. Cell Biol. 21, 452–460 (2009).

    Article  CAS  Google Scholar 

  27. Lewis, B.P., Burge, C.B. & Bartel, D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).

    Article  CAS  Google Scholar 

  28. Rehmsmeier, M., Steffen, P., Hochsmann, M. & Giegerich, R. Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507–1517 (2004).

    Article  CAS  Google Scholar 

  29. Miranda, K.C. et al. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203–1217 (2006).

    Article  CAS  Google Scholar 

  30. Wang, W.X., Wilfred, B.R., Hu, Y., Stromberg, A.J. & Nelson, P.T. Anti-Argonaute RIP-Chip shows that miRNA transfections alter global patterns of mRNA recruitment to microribonucleoprotein complexes. RNA 16, 394–404 (2010).

    Article  CAS  Google Scholar 

  31. Nonne, N., Ameyar-Zazoua, M., Souidi, M. & Harel-Bellan, A. Tandem affinity purification of miRNA target mRNAs (TAP-Tar). Nucleic Acids Res. 38, e20 (2010).

    Article  Google Scholar 

  32. Moore, L.M. & Zhang, W. Targeting miR-21 in glioma: a small RNA with big potential. Expert Opin. Ther. Targets 14, 1247–1257 (2010).

    Article  CAS  Google Scholar 

  33. Peters, L. & Meister, G. Argonaute proteins: mediators of RNA silencing. Mol. Cell 26, 611–623 (2007).

    Article  CAS  Google Scholar 

  34. York, I.A., Brehm, M.A., Zendzian, S., Towne, C.F. & Rock, K.L. Endoplasmic reticulum aminopeptidase 1 (ERAP1) trims MHC class I-presented peptides in vivo and plays an important role in immunodominance. Proc. Natl. Acad. Sci. USA 103, 9202–9207 (2006).

    Article  CAS  Google Scholar 

  35. Karttunen, J., Sanderson, S. & Shastri, N. Detection of rare antigen-presenting cells by the lacZ T-cell activation assay suggests an expression cloning strategy for T-cell antigens. Proc. Natl. Acad. Sci. USA 89, 6020–6024 (1992).

    Article  CAS  Google Scholar 

  36. Shastri, N. & Gonzalez, F. Endogenous generation and presentation of the ovalbumin peptide/Kb complex to T cells. J. Immunol. 150, 2724–2736 (1993).

    CAS  PubMed  Google Scholar 

  37. Firat, E. et al. The role of endoplasmic reticulum-associated aminopeptidase 1 in immunity to infection and in cross-presentation. J. Immunol. 178, 2241–2248 (2007).

    Article  CAS  Google Scholar 

  38. Yan, J. et al. In vivo role of ER-associated peptidase activity in tailoring peptides for presentation by MHC class Ia and class Ib molecules. J. Exp. Med. 203, 647–659 (2006).

    Article  CAS  Google Scholar 

  39. Blanchard, N. et al. Endoplasmic reticulum aminopeptidase associated with antigen processing defines the composition and structure of MHC class I peptide repertoire in normal and virus-infected cells. J. Immunol. 184, 3033–3042 (2010).

    Article  CAS  Google Scholar 

  40. Tanioka, T. et al. Human leukocyte-derived arginine aminopeptidase. The third member of the oxytocinase subfamily of aminopeptidases. J. Biol. Chem. 278, 32275–32283 (2003).

    Article  CAS  Google Scholar 

  41. Fruci, D. et al. Altered expression of endoplasmic reticulum aminopeptidases ERAP1 and ERAP2 in transformed non-lymphoid human tissues. J. Cell. Physiol. 216, 742–749 (2008).

    Article  CAS  Google Scholar 

  42. Georgiadou, D. et al. Placental leucine aminopeptidase efficiently generates mature antigenic peptides in vitro but in patterns distinct from endoplasmic reticulum aminopeptidase 1. J. Immunol. 185, 1584–1592 (2010).

    Article  CAS  Google Scholar 

  43. Hansen, S.G. et al. Evasion of CD8+ T cells is critical for superinfection by cytomegalovirus. Science 328, 102–106 (2010).

    Article  CAS  Google Scholar 

  44. Manley, T.J. et al. Immune evasion proteins of human cytomegalovirus do not prevent a diverse CD8+ cytotoxic T-cell response in natural infection. Blood 104, 1075–1082 (2004).

    Article  CAS  Google Scholar 

  45. Evnouchidou, I. et al. The internal sequence of the peptide-substrate determines its N-terminus trimming by ERAP1. PLoS ONE 3, e3658 (2008).

    Article  Google Scholar 

  46. Niles, A.L., Moravec, R.A. & Riss, T.L. In vitro viability and cytotoxicity testing and same-well multi-parametric combinations for high throughput screening. Curr Chem Genomics 3, 33–41 (2009).

    Article  CAS  Google Scholar 

  47. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank M. Tsujimoto (RIKEN, Wako) for recombinant human ERAP1 cDNA and polyclonal antibody to ERAP1; P. van Endert and L. Saveanu (Institut National de la Santé et de la Recherché Médicale, Paris) for monoclonal antibody 6H9 to ERAP1; I. York (Michigan State University) and K. Rock (University of Massachusetts Medical School) for pUG1-based vectors and technical help; N. Shastri (University of California, Berkeley) for the B3Z T cell hybridoma; T. Shenk (Princeton University) for pAD/Cre BAC; and C.-Y. Kang and T.-K. Kim for technical help. Supported by the Creative Research Initiatives Program of the Ministry of Science and Technology and the Korea Science and Engineering Foundation (K.A.), the Brain Korea 21 project of the Ministry of Education, Science and Technology of the Republic of Korea (S.K., S.L. and D.K.) and the US National Institutes of Health (CA18029 and AI053193 to S.R.R.).

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S.K., D.K., Y.-K.K. and V.N.K. designed and did biochemical and cell biological experiments; J.S. and Y.K. did microarray experiments; S.L., Y.-E.K. and J.-H.A. generated HCMV mutants; I.E. and E.S. did in vitro ERAP1 trimming assays; S.R.R. cloned the HCMV-specific CTLs; and S.K. and K.A. designed the overall study and wrote the paper.

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Correspondence to Kwangseog Ahn.

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Kim, S., Lee, S., Shin, J. et al. Human cytomegalovirus microRNA miR-US4-1 inhibits CD8+ T cell responses by targeting the aminopeptidase ERAP1. Nat Immunol 12, 984–991 (2011). https://doi.org/10.1038/ni.2097

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