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Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation

Nature Immunology volume 16, pages 838849 (2015) | Download Citation

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Abstract

Interferon-γ (IFN-γ) primes macrophages for enhanced microbial killing and inflammatory activation by Toll-like receptors (TLRs), but little is known about the regulation of cell metabolism or mRNA translation during this priming. We found that IFN-γ regulated the metabolism and mRNA translation of human macrophages by targeting the kinases mTORC1 and MNK, both of which converge on the selective regulator of translation initiation eIF4E. Physiological downregulation of mTORC1 by IFN-γ was associated with autophagy and translational suppression of repressors of inflammation such as HES1. Genome-wide ribosome profiling in TLR2-stimulated macrophages showed that IFN-γ selectively modulated the macrophage translatome to promote inflammation, further reprogram metabolic pathways and modulate protein synthesis. These results show that IFN-γ–mediated metabolic reprogramming and translational regulation are key components of classical inflammatory macrophage activation.

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References

  1. 1.

    & Cross-regulation of signaling pathways by interferon-γ: implications for immune responses and autoimmune diseases. Immunity 31, 539–550 (2009).

  2. 2.

    & The JAK-STAT pathway at twenty. Immunity 36, 503–514 (2012).

  3. 3.

    et al. IFN-γ suppresses IL-10 production and synergizes with TLR2 by regulating GSK3 and CREB/AP-1 proteins. Immunity 24, 563–574 (2006).

  4. 4.

    et al. Integrated regulation of Toll-like receptor responses by Notch and interferon-γ pathways. Immunity 29, 691–703 (2008).

  5. 5.

    et al. Latent enhancers activated by stimulation in differentiated cells. Cell 152, 157–171 (2013).

  6. 6.

    et al. Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and Toll-like receptor signaling. Immunity 39, 454–469 (2013).

  7. 7.

    , , , & Translational control of immune responses: from transcripts to translatomes. Nat. Immunol. 15, 503–511 (2014).

  8. 8.

    et al. Interleukin-1 receptor-associated kinase 2 is critical for lipopolysaccharide-mediated post-transcriptional control. J. Biol. Chem. 284, 10367–10375 (2009).

  9. 9.

    et al. Notch-RBP-J signaling regulates the transcription factor IRF8 to promote inflammatory macrophage polarization. Nat. Immunol. 13, 642–650 (2012).

  10. 10.

    et al. Translational control of the activation of transcription factor NF-κB and production of type I interferon by phosphorylation of the translation factor eIF4E. Nat. Immunol. 13, 543–550 (2012).

  11. 11.

    et al. Translational control of the innate immune response through IRF-7. Nature 452, 323–328 (2008).

  12. 12.

    et al. Apoptosis resistance downstream of eIF4E: posttranscriptional activation of an anti-apoptotic transcript carrying a consensus hairpin structure. Nucleic Acids Res. 34, 4375–4386 (2006).

  13. 13.

    & Regulation of type I interferon responses. Nat. Rev. Immunol. 14, 36–49 (2014).

  14. 14.

    & Host translation at the nexus of infection and immunity. Cell Host Microbe 12, 470–483 (2012).

  15. 15.

    et al. A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 472, 481–485 (2011).

  16. 16.

    , , , & Regulation of interferon-dependent mRNA translation of target genes. J. Interferon Cytokine Res. 34, 289–296 (2014).

  17. 17.

    , , , & The GAIT system: a gatekeeper of inflammatory gene expression. Trends Biochem. Sci. 34, 324–331 (2009).

  18. 18.

    & mTOR signaling in growth control and disease. Cell 149, 274–293 (2012).

  19. 19.

    et al. The TSC-mTOR signaling pathway regulates the innate inflammatory response. Immunity 29, 565–577 (2008).

  20. 20.

    et al. mTOR and GSK-3 shape the CD4+ T-cell stimulatory and differentiation capacity of myeloid DCs after exposure to LPS. Blood 115, 4758–4769 (2010).

  21. 21.

    , & Regulation of interferon and Toll-like receptor signaling during macrophage activation by opposing feedforward and feedback inhibition mechanisms. Immunol. Rev. 226, 41–56 (2008).

  22. 22.

    et al. Phosphorylation of eukaryotic protein synthesis initiation factor 4E at Ser-209. J. Biol. Chem. 270, 14597–14603 (1995).

  23. 23.

    et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 485, 55–61 (2012).

  24. 24.

    , & Autophagy in infection, inflammation and immunity. Nat. Rev. Immunol. 13, 722–737 (2013).

  25. 25.

    et al. mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase. Science 334, 678–683 (2011).

  26. 26.

    , , & Ragulator is a GEF for the rag GTPases that signal amino acid levels to mTORC1. Cell 150, 1196–1208 (2012).

  27. 27.

    et al. Amino acid sufficiency and mTOR regulate p70 S6 kinase and eIF-4E BP1 through a common effector mechanism. J. Biol. Chem. 273, 14484–14494 (1998).

  28. 28.

    & Relationship between interferon-γ, indoleamine 2,3-dioxygenase, and tryptophan catabolism. FASEB J. 5, 2516–2522 (1991).

  29. 29.

    & IDO expression by dendritic cells: tolerance and tryptophan catabolism. Nat. Rev. Immunol. 4, 762–774 (2004).

  30. 30.

    , , & Regulation of immune responses by mTOR. Annu. Rev. Immunol. 30, 39–68 (2012).

  31. 31.

    et al. Inhibition of RANK expression and osteoclastogenesis by TLRs and IFN-γ in human osteoclast precursors. J. Immunol. 183, 7223–7233 (2009).

  32. 32.

    , , & Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009).

  33. 33.

    et al. A unifying model for mTORC1-mediated regulation of mRNA translation. Nature 485, 109–113 (2012).

  34. 34.

    , & Protein synthesis rate is the predominant regulator of protein expression during differentiation. Mol. Syst. Biol. 9, 689 (2013).

  35. 35.

    et al. Leucyl-tRNA synthetase is an intracellular leucine sensor for the mTORC1-signaling pathway. Cell 149, 410–424 (2012).

  36. 36.

    , & An epigenetic switch involving NF-κB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation. Cell 139, 693–706 (2009).

  37. 37.

    et al. Amino acid starvation induced by invasive bacterial pathogens triggers an innate host defense program. Cell Host Microbe 11, 563–575 (2012).

  38. 38.

    & Pathogen signatures activate a ubiquitination pathway that modulates the function of the metabolic checkpoint kinase mTOR. Nat. Immunol. 14, 1219–1228 (2013).

  39. 39.

    & Metabolism of inflammation limited by AMPK and pseudo-starvation. Nature 493, 346–355 (2013).

  40. 40.

    & Metabolic regulation of immune responses. Annu. Rev. Immunol. 32, 609–634 (2014).

  41. 41.

    , & Translating glycolytic metabolism to innate immunity in dendritic cells. Cell Metab. 19, 737–739 (2014).

  42. 42.

    Glycolytic reprogramming by TLRs in dendritic cells. Nat. Immunol. 15, 314–315 (2014).

  43. 43.

    & The M1 and M2 paradigm of macrophage activation: time for reassessment. F1000Prime Rep. 6, 13 (2014).

  44. 44.

    et al. Rapamycin unbalances the polarization of human macrophages to M1. Immunology 140, 179–190 (2013).

  45. 45.

    et al. The TSC-mTOR pathway regulates macrophage polarization. Nat. Commun. 4, 2834 (2013).

  46. 46.

    et al. mTOR- and HIF-1α-mediated aerobic glycolysis as metabolic basis for trained immunity. Science 345, 1250684 (2014).

  47. 47.

    & Translation inhibition and metabolic stress pathways in the host response to bacterial pathogens. Nat. Rev. Microbiol. 11, 365–369 (2013).

  48. 48.

    et al. Human tRNA synthetase catalytic nulls with diverse functions. Science 345, 328–332 (2014).

  49. 49.

    , , , & The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534–1550 (2012).

  50. 50.

    , & edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).

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Acknowledgements

We thank members of the Weill Cornell Medical College Genomics Core for advice about RNA-Seq, J. Schulze (UC Davis Proteomics Core) for advice about amino acid measurements, B. Zhao and L. Donlin for review of the manuscript, K. Park-Min (Hospital for Special Surgery, New York, New York, USA) for providing Myc inhibitor and siRNA oligos, and S. Park and Y. Qiao for discussion about bioinformatic analysis. This work was supported by the NIH (grants to L.B.I. and C.M.R.), the Leonard Tow Foundation (grant to the David Z. Rosensweig Genomics Research Center), the Greenberg Medical Research Institute, the Starr Foundation (grant to C.M.R.) and the European Commission (EU PITN-GA-2012-316861 to Y.Z.).

Author information

Author notes

    • Xiaodi Su
    •  & Yingpu Yu

    These authors contributed equally to this work.

Affiliations

  1. Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA.

    • Xiaodi Su
    •  & Lionel B Ivashkiv
  2. Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA.

    • Xiaodi Su
    • , Eugenia G Giannopoulou
    • , Xiaoyu Hu
    •  & Lionel B Ivashkiv
  3. Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, New York, USA.

    • Yingpu Yu
    •  & Charles M Rice
  4. Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Yi Zhong
    •  & Gunnar Rätsch
  5. Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, New York, USA.

    • Eugenia G Giannopoulou
  6. Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Hui Liu
    •  & Justin R Cross

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Contributions

X.S. designed and conducted experiments, analyzed data and prepared the manuscript; Y.Y. performed polysome-profiling and ribosome-profiling experiments and analyzed data; Y.Z. analyzed ribosome-profiling, RNA-Seq and miRNA-Seq data; E.G.G. analyzed ribosome-profiling and RNA-Seq data; J.R.C. and H.L. performed liquid chromatography–mass spectrometry experiments and analyzed data; X.H., G.R. and C.M.R. provided advice about experiments and data analysis and contributed to manuscript preparation; L.B.I. conceived and supervised experiments and prepared the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Lionel B Ivashkiv.

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    Supplementary Text and Figures

    Supplementary Figures 1–8 and Supplementary Tables 3 and 4

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    Supplementary Table 1

    Metabolic genes whose translation was increased or suppressed by IFN-γ Genes contained in blue wedge in pie chart in Supplementary Fig. 7a-b

  2. 2.

    Supplementary Table 2

    Immune genes whose translation was increased or suppressed by IFN-γ Genes contained in red wedge in pie chart in Supplementary Fig. 7a-b

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DOI

https://doi.org/10.1038/ni.3205

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