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  • Review Article
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Post-transcriptional checkpoints in autoimmunity

Abstract

Post-transcriptional regulation is a fundamental process in gene expression that has a role in diverse cellular processes, including immune responses. A core concept underlying post-transcriptional regulation is that protein abundance is not solely determined by transcript abundance. Indeed, transcription and translation are not directly coupled, and intervening steps occur between these processes, including the regulation of mRNA stability, localization and alternative splicing, which can impact protein abundance. These steps are controlled by various post-transcription factors such as RNA-binding proteins and non-coding RNAs, including microRNAs, and aberrant post-transcriptional regulation has been implicated in various pathological conditions. Indeed, studies on the pathogenesis of autoimmune and inflammatory diseases have identified various post-transcription factors as important regulators of immune cell-mediated and target effector cell-mediated pathological conditions. This Review summarizes current knowledge regarding the roles of post-transcriptional checkpoints in autoimmunity, as evidenced by studies in both haematopoietic and non-haematopoietic cells, and discusses the relevance of these findings for developing new anti-inflammatory therapies.

Key points

  • Post-transcriptional regulation of gene expression is an important step in controlling various cellular processes, including immune-related processes, and disruption of post-transcriptional regulation can lead to aberrant cell responses.

  • Redundant, cooperative and antagonistic post-transcriptional regulators control the expression of immune-related mRNA transcripts, enabling the fine-tuning of inflammatory responses.

  • Post-transcriptional checkpoints are involved in the regulation of antibody-mediated autoimmunity and T cell-mediated autoimmunity.

  • Post-transcriptional checkpoints in non-haematopoietic cells might also contribute to autoimmune manifestations.

  • Specific post-transcriptional regulators are abnormally expressed or function aberrantly in various systemic or organ-specific autoimmune conditions.

  • Additional mechanistic and translational research is needed to therapeutically harness the post-transcriptional pathway.

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Fig. 1: Post-transcriptional checkpoints in the development of autoimmunity.
Fig. 2: RNA-binding proteins regulate the expression of immune-related mRNA.
Fig. 3: Post-transcriptional checkpoints in antibody-mediated autoimmunity.
Fig. 4: Post-transcriptional checkpoints in T cell-mediated autoimmunity.

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References

  1. Theofilopoulos, A. N., Kono, D. H. & Baccala, R. The multiple pathways to autoimmunity. Nat. Immunol. 18, 716–724 (2017).

    CAS  PubMed Central  PubMed  Google Scholar 

  2. Cho, J. H. & Gregersen, P. K. Genomics and the multifactorial nature of human autoimmune disease. N. Engl. J. Med. 365, 1612–1623 (2011).

    CAS  PubMed  Google Scholar 

  3. Fugger, L., Jensen, L. T. & Rossjohn, J. Challenges, progress, and prospects of developing therapies to treat autoimmune diseases. Cell 181, 63–80 (2020).

    CAS  PubMed  Google Scholar 

  4. Steinman, L. Immunology of relapse and remission in multiple sclerosis. Annu. Rev. Immunol. 32, 257–281 (2014).

    CAS  PubMed  Google Scholar 

  5. Szekanecz, Z. et al. Autoinflammation and autoimmunity across rheumatic and musculoskeletal diseases. Nat. Rev. Rheumatol. 17, 585–595 (2021).

    CAS  PubMed  Google Scholar 

  6. Buccitelli, C. & Selbach, M. mRNAs, proteins and the emerging principles of gene expression control. Nat. Rev. Genet. 21, 630–644 (2020).

    CAS  PubMed  Google Scholar 

  7. Nicolet, B. P. & Wolkers, M. C. The relationship of mRNA with protein expression in CD8+ T cells associates with gene class and gene characteristics. PLoS One 17, e0276294 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  8. Jiang, L. et al. A quantitative proteome map of the human body. Cell 183, 269–283.e19 (2020).

    CAS  PubMed Central  PubMed  Google Scholar 

  9. Muller-McNicoll, M. & Neugebauer, K. M. How cells get the message: dynamic assembly and function of mRNA–protein complexes. Nat. Rev. Genet. 14, 275–287 (2013).

    PubMed  Google Scholar 

  10. Gokhale, N. S., Smith, J. R., Van Gelder, R. D. & Savan, R. RNA regulatory mechanisms that control antiviral innate immunity. Immunol. Rev. 304, 77–96 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  11. Turner, M. & Diaz-Munoz, M. D. RNA-binding proteins control gene expression and cell fate in the immune system. Nat. Immunol. 19, 120–129 (2018).

    CAS  PubMed  Google Scholar 

  12. Carpenter, S., Ricci, E. P., Mercier, B. C., Moore, M. J. & Fitzgerald, K. A. Post-transcriptional regulation of gene expression in innate immunity. Nat. Rev. Immunol. 14, 361–376 (2014).

    CAS  PubMed  Google Scholar 

  13. Mehta, A. & Baltimore, D. MicroRNAs as regulatory elements in immune system logic. Nat. Rev. Immunol. 16, 279–294 (2016).

    CAS  PubMed  Google Scholar 

  14. Jurgens, A. P., Popovic, B. & Wolkers, M. C. T cells at work: how post-transcriptional mechanisms control T cell homeostasis and activation. Eur. J. Immunol. 51, 2178–2187 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  15. O’Connell, R. M., Rao, D. S., Chaudhuri, A. A. & Baltimore, D. Physiological and pathological roles for microRNAs in the immune system. Nat. Rev. Immunol. 10, 111–122 (2010).

    PubMed  Google Scholar 

  16. Xiao, C. & Rajewsky, K. MicroRNA control in the immune system: basic principles. Cell 136, 26–36 (2009).

    CAS  PubMed  Google Scholar 

  17. Anderson, P. Post-transcriptional control of cytokine production. Nat. Immunol. 9, 353–359 (2008).

    CAS  PubMed  Google Scholar 

  18. Stoecklin, G. & Anderson, P. In a tight spot: ARE-mRNAs at processing bodies. Genes. Dev. 21, 627–631 (2007).

    CAS  PubMed  Google Scholar 

  19. Raghavan, A. et al. Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res. 30, 5529–5538 (2002).

    CAS  PubMed Central  PubMed  Google Scholar 

  20. Yoshinaga, M. & Takeuchi, O. Post-transcriptional control of immune responses and its potential application. Clin. Transl. Immunol. 8, e1063 (2019).

    Google Scholar 

  21. Corley, M., Burns, M. C. & Yeo, G. W. How RNA-binding proteins interact with RNA: molecules and mechanisms. Mol. Cell 78, 9–29 (2020).

    CAS  PubMed Central  PubMed  Google Scholar 

  22. 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).

    CAS  PubMed  Google Scholar 

  23. Gerstberger, S., Hafner, M. & Tuschl, T. A census of human RNA-binding proteins. Nat. Rev. Genet. 15, 829–845 (2014).

    CAS  PubMed  Google Scholar 

  24. Alles, J. et al. An estimate of the total number of true human miRNAs. Nucleic Acids Res. 47, 3353–3364 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  25. Frye, M., Harada, B. T., Behm, M. & He, C. RNA modifications modulate gene expression during development. Science 361, 1346–1349 (2018).

    CAS  PubMed Central  PubMed  Google Scholar 

  26. Murray, P. J. Macrophage polarization. Annu. Rev. Physiol. 79, 541–566 (2017).

    CAS  PubMed  Google Scholar 

  27. Petersone, L. et al. T cell/B cell collaboration and autoimmunity: an intimate relationship. Front. Immunol. 9, 1941 (2018).

    PubMed Central  PubMed  Google Scholar 

  28. Chemin, K., Gerstner, C. & Malmstrom, V. Effector functions of CD4+ T cells at the site of local autoimmune inflammation-lessons from rheumatoid arthritis. Front. Immunol. 10, 353 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  29. Arbuckle, M. R. et al. Development of autoantibodies before the clinical onset of systemic lupus erythematosus. N. Engl. J. Med. 349, 1526–1533 (2003).

    CAS  PubMed  Google Scholar 

  30. McInnes, I. B. & Schett, G. The pathogenesis of rheumatoid arthritis. N. Engl. J. Med. 365, 2205–2219 (2011).

    CAS  PubMed  Google Scholar 

  31. Dorner, T., Giesecke, C. & Lipsky, P. E. Mechanisms of B cell autoimmunity in SLE. Arthritis Res. Ther. 13, 243 (2011).

    PubMed Central  PubMed  Google Scholar 

  32. Winter, O., Dame, C., Jundt, F. & Hiepe, F. Pathogenic long-lived plasma cells and their survival niches in autoimmunity, malignancy, and allergy. J. Immunol. 189, 5105–5111 (2012).

    CAS  PubMed  Google Scholar 

  33. William, J., Euler, C. & Shlomchik, M. J. Short-lived plasmablasts dominate the early spontaneous rheumatoid factor response: differentiation pathways, hypermutating cell types, and affinity maturation outside the germinal center. J. Immunol. 174, 6879–6887 (2005).

    CAS  PubMed  Google Scholar 

  34. Eisenberg, R. & Albert, D. B-cell targeted therapies in rheumatoid arthritis and systemic lupus erythematosus. Nat. Clin. Pract. Rheumatol. 2, 20–27 (2006).

    CAS  PubMed  Google Scholar 

  35. Edwards, J. C. & Cambridge, G. B-cell targeting in rheumatoid arthritis and other autoimmune diseases. Nat. Rev. Immunol. 6, 394–403 (2006).

    CAS  PubMed  Google Scholar 

  36. Mariette, X. et al. A randomized, phase II study of sequential belimumab and rituximab in primary Sjögren’s syndrome. JCI Insight https://doi.org/10.1172/jci.insight.163030 (2022).

    Article  PubMed Central  PubMed  Google Scholar 

  37. Rubin, S. J. S., Bloom, M. S. & Robinson, W. H. B cell checkpoints in autoimmune rheumatic diseases. Nat. Rev. Rheumatol. 15, 303–315 (2019).

    PubMed  Google Scholar 

  38. Lee, D. S. W., Rojas, O. L. & Gommerman, J. L. B cell depletion therapies in autoimmune disease: advances and mechanistic insights. Nat. Rev. Drug Discov. 20, 179–199 (2021).

    CAS  PubMed  Google Scholar 

  39. Nutt, S. L., Hodgkin, P. D., Tarlinton, D. M. & Corcoran, L. M. The generation of antibody-secreting plasma cells. Nat. Rev. Immunol. 15, 160–171 (2015).

    CAS  PubMed  Google Scholar 

  40. Ise, W. & Kurosaki, T. Plasma cell differentiation during the germinal center reaction. Immunol. Rev. 288, 64–74 (2019).

    CAS  PubMed  Google Scholar 

  41. Zandhuis, N. D., Nicolet, B. P. & Wolkers, M. C. RNA-binding protein expression alters upon differentiation of human B cells and T cells. Front. Immunol. 12, 717324 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  42. Galloway, A. et al. RNA-binding proteins ZFP36L1 and ZFP36L2 promote cell quiescence. Science 352, 453–459 (2016).

    CAS  PubMed  Google Scholar 

  43. Chang, X., Li, B. & Rao, A. RNA-binding protein hnRNPLL regulates mRNA splicing and stability during B-cell to plasma-cell differentiation. Proc. Natl Acad. Sci. USA 112, E1888–E1897 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  44. Saveliev, A., Bell, S. E. & Turner, M. Efficient homing of antibody-secreting cells to the bone marrow requires RNA-binding protein ZFP36L1. J. Exp. Med. https://doi.org/10.1084/jem.20200504 (2021).

    Article  PubMed  Google Scholar 

  45. Newman, R. et al. Maintenance of the marginal-zone B cell compartment specifically requires the RNA-binding protein ZFP36L1. Nat. Immunol. 18, 683–693 (2017).

    CAS  PubMed Central  PubMed  Google Scholar 

  46. Caro-Maldonado, A. et al. Metabolic reprogramming is required for antibody production that is suppressed in anergic but exaggerated in chronically BAFF-exposed B cells. J. Immunol. 192, 3626–3636 (2014).

    CAS  PubMed  Google Scholar 

  47. Blair, D., Dufort, F. J. & Chiles, T. C. Protein kinase Cβ is critical for the metabolic switch to glycolysis following B-cell antigen receptor engagement. Biochem. J. 448, 165–169 (2012).

    CAS  PubMed  Google Scholar 

  48. Pearce, E. L., Poffenberger, M. C., Chang, C. H. & Jones, R. G. Fueling immunity: insights into metabolism and lymphocyte function. Science 342, 1242454 (2013).

    PubMed Central  PubMed  Google Scholar 

  49. Diaz-Munoz, M. D. et al. The RNA-binding protein HuR is essential for the B cell antibody response. Nat. Immunol. 16, 415–425 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  50. DeMicco, A. et al. B Cell-intrinsic expression of the HuR RNA-binding protein is required for the T cell-dependent immune response in vivo. J. Immunol. 195, 3449–3462 (2015).

    CAS  PubMed  Google Scholar 

  51. Monzon-Casanova, E. et al. The RNA-binding protein PTBP1 is necessary for B cell selection in germinal centers. Nat. Immunol. 19, 267–278 (2018).

    CAS  PubMed Central  PubMed  Google Scholar 

  52. Liu, N. & Pan, T. N6-methyladenosine-encoded epitranscriptomics. Nat. Struct. Mol. Biol. 23, 98–102 (2016).

    CAS  PubMed  Google Scholar 

  53. Bechara, R. & Gaffen, S. L. ‘(m6)A’ stands for ‘autoimmunity’: reading, writing, and erasing RNA modifications during inflammation. Trends Immunol. https://doi.org/10.1016/j.it.2021.10.002 (2021).

    Article  PubMed Central  PubMed  Google Scholar 

  54. Shulman, Z. & Stern-Ginossar, N. The RNA modification N6-methyladenosine as a novel regulator of the immune system. Nat. Immunol. 21, 501–512 (2020).

    CAS  PubMed  Google Scholar 

  55. Boulias, K. & Greer, E. L. Biological roles of adenine methylation in RNA. Nat. Rev. Genet. https://doi.org/10.1038/s41576-022-00534-0 (2022).

    Article  PubMed Central  PubMed  Google Scholar 

  56. Grenov, A. C. et al. The germinal center reaction depends on RNA methylation and divergent functions of specific methyl readers. J. Exp. Med. https://doi.org/10.1084/jem.20210360 (2021).

    Article  PubMed Central  PubMed  Google Scholar 

  57. Turner, D. J. et al. A functional screen of RNA binding proteins identifies genes that promote or limit the accumulation of CD138+ plasma cells. Elife https://doi.org/10.7554/eLife.72313 (2022).

    Article  PubMed Central  PubMed  Google Scholar 

  58. Zaccara, S. & Jaffrey, S. R. A unified model for the function of YTHDF proteins in regulating m6A-modified mRNA. Cell 181, 1582–1595.e18 (2020).

    CAS  PubMed Central  PubMed  Google Scholar 

  59. Matsushita, K. et al. Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Nature 458, 1185–1190 (2009).

    CAS  PubMed  Google Scholar 

  60. Bhat, N. et al. Regnase-1 is essential for B cell homeostasis to prevent immunopathology. J. Exp. Med. https://doi.org/10.1084/jem.20200971 (2021).

    Article  PubMed Central  PubMed  Google Scholar 

  61. Ise, W. et al. The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cells. Nat. Immunol. 12, 536–543 (2011).

    CAS  PubMed Central  PubMed  Google Scholar 

  62. Betz, B. C. et al. Batf coordinates multiple aspects of B and T cell function required for normal antibody responses. J. Exp. Med. 207, 933–942 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  63. Yin, Z. et al. RNA-binding motifs of hnRNP K are critical for induction of antibody diversification by activation-induced cytidine deaminase. Proc. Natl Acad. Sci. USA 117, 11624–11635 (2020).

    CAS  PubMed Central  PubMed  Google Scholar 

  64. Hu, W., Begum, N. A., Mondal, S., Stanlie, A. & Honjo, T. Identification of DNA cleavage- and recombination-specific hnRNP cofactors for activation-induced cytidine deaminase. Proc. Natl Acad. Sci. USA 112, 5791–5796 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  65. Jeker, L. T. & Bluestone, J. A. MicroRNA regulation of T-cell differentiation and function. Immunol. Rev. 253, 65–81 (2013).

    PubMed Central  PubMed  Google Scholar 

  66. Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A. & Burge, C. B. Proliferating cells express mRNAs with shortened 3’ untranslated regions and fewer microRNA target sites. Science 320, 1643–1647 (2008).

    CAS  PubMed Central  PubMed  Google Scholar 

  67. de Yebenes, V. G., Bartolome-Izquierdo, N. & Ramiro, A. R. Regulation of B-cell development and function by microRNAs. Immunol. Rev. 253, 25–39 (2013).

    PubMed Central  PubMed  Google Scholar 

  68. Basso, K. et al. Identification of the human mature B cell miRNome. Immunity 30, 744–752 (2009).

    CAS  PubMed Central  PubMed  Google Scholar 

  69. Koralov, S. B. et al. Dicer ablation affects antibody diversity and cell survival in the B lymphocyte lineage. Cell 132, 860–874 (2008).

    CAS  PubMed  Google Scholar 

  70. Belver, L., de Yebenes, V. G. & Ramiro, A. R. MicroRNAs prevent the generation of autoreactive antibodies. Immunity 33, 713–722 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  71. Xu, S., Guo, K., Zeng, Q., Huo, J. & Lam, K. P. The RNase III enzyme Dicer is essential for germinal center B-cell formation. Blood 119, 767–776 (2012).

    CAS  PubMed  Google Scholar 

  72. Ventura, A. et al. Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell 132, 875–886 (2008).

    CAS  PubMed Central  PubMed  Google Scholar 

  73. Rao, D. S. et al. MicroRNA-34a perturbs B lymphocyte development by repressing the forkhead box transcription factor Foxp1. Immunity 33, 48–59 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  74. Gururajan, M. et al. MicroRNA 125b inhibition of B cell differentiation in germinal centers. Int. Immunol. 22, 583–592 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  75. Porstner, M. et al. miR-148a promotes plasma cell differentiation and targets the germinal center transcription factors Mitf and Bach2. Eur. J. Immunol. 45, 1206–1215 (2015).

    CAS  PubMed  Google Scholar 

  76. Rodriguez, A. et al. Requirement of bic/microRNA-155 for normal immune function. Science 316, 608–611 (2007).

    CAS  PubMed Central  PubMed  Google Scholar 

  77. Thai, T. H. et al. Regulation of the germinal center response by microRNA-155. Science 316, 604–608 (2007).

    CAS  PubMed  Google Scholar 

  78. Lu, D. et al. The miR-155-PU.1 axis acts on Pax5 to enable efficient terminal B cell differentiation. J. Exp. Med. 211, 2183–2198 (2014).

    CAS  PubMed Central  PubMed  Google Scholar 

  79. Kuchen, S. et al. Regulation of microRNA expression and abundance during lymphopoiesis. Immunity 32, 828–839 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  80. Vigorito, E. et al. microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells. Immunity 27, 847–859 (2007).

    CAS  PubMed Central  PubMed  Google Scholar 

  81. Dorsett, Y. et al. MicroRNA-155 suppresses activation-induced cytidine deaminase-mediated Myc-Igh translocation. Immunity 28, 630–638 (2008).

    CAS  PubMed Central  PubMed  Google Scholar 

  82. Teng, G. et al. MicroRNA-155 is a negative regulator of activation-induced cytidine deaminase. Immunity 28, 621–629 (2008).

    CAS  PubMed Central  PubMed  Google Scholar 

  83. Walker, L. S. K. The link between circulating follicular helper T cells and autoimmunity. Nat. Rev. Immunol. https://doi.org/10.1038/s41577-022-00693-5 (2022).

    Article  PubMed Central  PubMed  Google Scholar 

  84. Patel, P. S. et al. Translational regulation of TFH cell differentiation and autoimmune pathogenesis. Sci. Adv. 8, eabo1782 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  85. Ueno, H. T follicular helper cells in human autoimmunity. Curr. Opin. Immunol. 43, 24–31 (2016).

    CAS  PubMed  Google Scholar 

  86. Vazquez, M. I., Catalan-Dibene, J. & Zlotnik, A. B cells responses and cytokine production are regulated by their immune microenvironment. Cytokine 74, 318–326 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  87. Cyster, J. G. & Allen, C. D. C. B cell responses: cell interaction dynamics and decisions. Cell 177, 524–540 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  88. Schneider, P. et al. BAFF, a novel ligand of the tumor necrosis factor family, stimulates B cell growth. J. Exp. Med. 189, 1747–1756 (1999).

    CAS  PubMed Central  PubMed  Google Scholar 

  89. Mackay, F. & Schneider, P. Cracking the BAFF code. Nat. Rev. Immunol. 9, 491–502 (2009).

    CAS  PubMed  Google Scholar 

  90. Mackay, F. & Browning, J. L. BAFF: a fundamental survival factor for B cells. Nat. Rev. Immunol. 2, 465–475 (2002).

    CAS  PubMed  Google Scholar 

  91. Gorelik, L. et al. Normal B cell homeostasis requires B cell activation factor production by radiation-resistant cells. J. Exp. Med. 198, 937–945 (2003).

    CAS  PubMed Central  PubMed  Google Scholar 

  92. Steri, M. et al. Overexpression of the cytokine BAFF and autoimmunity risk. N. Engl. J. Med. 376, 1615–1626 (2017).

    CAS  PubMed Central  PubMed  Google Scholar 

  93. Vincent, F. B., Morand, E. F., Schneider, P. & Mackay, F. The BAFF/APRIL system in SLE pathogenesis. Nat. Rev. Rheumatol. 10, 365–373 (2014).

    CAS  PubMed  Google Scholar 

  94. Varin, M. M. et al. B-cell tolerance breakdown in Sjögren’s syndrome: focus on BAFF. Autoimmun. Rev. 9, 604–608 (2010).

    CAS  PubMed  Google Scholar 

  95. Nocturne, G. & Mariette, X. B cells in the pathogenesis of primary Sjögren syndrome. Nat. Rev. Rheumatol. 14, 133–145 (2018).

    CAS  PubMed  Google Scholar 

  96. Vinuesa, C. G. et al. A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity. Nature 435, 452–458 (2005).

    CAS  PubMed  Google Scholar 

  97. Glasmacher, E. et al. Roquin binds inducible costimulator mRNA and effectors of mRNA decay to induce microRNA-independent post-transcriptional repression. Nat. Immunol. 11, 725–733 (2010).

    CAS  PubMed  Google Scholar 

  98. Vogel, K. U. et al. Roquin paralogs 1 and 2 redundantly repress the Icos and Ox40 costimulator mRNAs and control follicular helper T cell differentiation. Immunity 38, 655–668 (2013).

    CAS  PubMed  Google Scholar 

  99. Yu, D. et al. Roquin represses autoimmunity by limiting inducible T-cell co-stimulator messenger RNA. Nature 450, 299–303 (2007).

    CAS  PubMed  Google Scholar 

  100. Qi, H., Cannons, J. L., Klauschen, F., Schwartzberg, P. L. & Germain, R. N. SAP-controlled T–B cell interactions underlie germinal centre formation. Nature 455, 764–769 (2008).

    CAS  PubMed Central  PubMed  Google Scholar 

  101. Linterman, M. A. et al. Follicular helper T cells are required for systemic autoimmunity. J. Exp. Med. 206, 561–576 (2009).

    CAS  PubMed Central  PubMed  Google Scholar 

  102. Essig, K. et al. Roquin targets mRNAs in a 3’-UTR-specific manner by different modes of regulation. Nat. Commun. 9, 3810 (2018).

    PubMed Central  PubMed  Google Scholar 

  103. Jeltsch, K. M. et al. Cleavage of roquin and regnase-1 by the paracaspase MALT1 releases their cooperatively repressed targets to promote TH17 differentiation. Nat. Immunol. 15, 1079–1089 (2014).

    CAS  PubMed  Google Scholar 

  104. Uehata, T. et al. Malt1-induced cleavage of regnase-1 in CD4+ helper T cells regulates immune activation. Cell 153, 1036–1049 (2013).

    CAS  PubMed  Google Scholar 

  105. Moore, M. J. et al. ZFP36 RNA-binding proteins restrain T cell activation and anti-viral immunity. Elife https://doi.org/10.7554/eLife.33057 (2018).

    Article  PubMed Central  PubMed  Google Scholar 

  106. Srivastava, M. et al. Roquin binds microRNA-146a and Argonaute2 to regulate microRNA homeostasis. Nat. Commun. 6, 6253 (2015).

    CAS  PubMed  Google Scholar 

  107. Pratama, A. et al. MicroRNA-146a regulates ICOS–ICOSL signalling to limit accumulation of T follicular helper cells and germinal centres. Nat. Commun. 6, 6436 (2015).

    CAS  PubMed  Google Scholar 

  108. Zhu, Y. et al. The E3 ligase VHL promotes follicular helper T cell differentiation via glycolytic-epigenetic control. J. Exp. Med. 216, 1664–1681 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  109. Yao, Y. et al. METTL3-dependent m6A modification programs T follicular helper cell differentiation. Nat. Commun. 12, 1333 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  110. Liu, N. et al. N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518, 560–564 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  111. Zaccara, S., Ries, R. J. & Jaffrey, S. R. Reading, writing and erasing mRNA methylation. Nat. Rev. Mol. Cell Biol. 20, 608–624 (2019).

    CAS  PubMed  Google Scholar 

  112. Edupuganti, R. R. et al. N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis. Nat. Struct. Mol. Biol. 24, 870–878 (2017).

    CAS  PubMed Central  PubMed  Google Scholar 

  113. Gebauer, F. & Hentze, M. W. Molecular mechanisms of translational control. Nat. Rev. Mol. Cell Biol. 5, 827–835 (2004).

    CAS  PubMed Central  PubMed  Google Scholar 

  114. Truitt, M. L. et al. Differential requirements for eIF4E dose in normal development and cancer. Cell 162, 59–71 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  115. Shen, S. et al. An epitranscriptomic mechanism underlies selective mRNA translation remodelling in melanoma persister cells. Nat. Commun. 10, 5713 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  116. Scapini, P. et al. G-CSF-stimulated neutrophils are a prominent source of functional BLyS. J. Exp. Med. 197, 297–302 (2003).

    CAS  PubMed Central  PubMed  Google Scholar 

  117. Huard, B. et al. BAFF production by antigen-presenting cells provides T cell co-stimulation. Int. Immunol. 16, 467–475 (2004).

    CAS  PubMed  Google Scholar 

  118. Craxton, A., Magaletti, D., Ryan, E. J. & Clark, E. A. Macrophage- and dendritic cell–dependent regulation of human B-cell proliferation requires the TNF family ligand BAFF. Blood 101, 4464–4471 (2003).

    CAS  PubMed  Google Scholar 

  119. Chu, V. T., Enghard, P., Riemekasten, G. & Berek, C. In vitro and in vivo activation induces BAFF and APRIL expression in B cells. J. Immunol. 179, 5947–5957 (2007).

    CAS  PubMed  Google Scholar 

  120. Ittah, M. et al. B cell-activating factor of the tumor necrosis factor family (BAFF) is expressed under stimulation by interferon in salivary gland epithelial cells in primary Sjögren’s syndrome. Arthritis Res. Ther. 8, R51 (2006).

    PubMed Central  PubMed  Google Scholar 

  121. Kato, A., Truong-Tran, A. Q., Scott, A. L., Matsumoto, K. & Schleimer, R. P. Airway epithelial cells produce B cell-activating factor of TNF family by an IFN-β-dependent mechanism. J. Immunol. 177, 7164–7172 (2006).

    CAS  PubMed  Google Scholar 

  122. Idda, M. L. et al. Cooperative translational control of polymorphic BAFF by NF90 and miR-15a. Nucleic Acids Res. 46, 12040–12051 (2018).

    PubMed Central  PubMed  Google Scholar 

  123. Liblau, R. S., Wong, F. S., Mars, L. T. & Santamaria, P. Autoreactive CD8 T cells in organ-specific autoimmunity: emerging targets for therapeutic intervention. Immunity 17, 1–6 (2002).

    CAS  PubMed  Google Scholar 

  124. Krovi, S. H. & Kuchroo, V. K. Activation pathways that drive CD4+ T cells to break tolerance in autoimmune diseases. Immunol. Rev. 307, 161–190 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  125. Rodriguez-Galan, A., Fernandez-Messina, L. & Sanchez-Madrid, F. Control of immunoregulatory molecules by miRNAs in T cell activation. Front. Immunol. 9, 2148 (2018).

    PubMed Central  PubMed  Google Scholar 

  126. Wu, H. et al. miRNA profiling of naive, effector and memory CD8 T cells. PLoS One 2, e1020 (2007).

    PubMed Central  PubMed  Google Scholar 

  127. Muljo, S. A. et al. Aberrant T cell differentiation in the absence of Dicer. J. Exp. Med. 202, 261–269 (2005).

    CAS  PubMed Central  PubMed  Google Scholar 

  128. Zhang, N. & Bevan, M. J. Dicer controls CD8+ T-cell activation, migration, and survival. Proc. Natl Acad. Sci. USA 107, 21629–21634 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  129. Yang, L. et al. miR-146a controls the resolution of T cell responses in mice. J. Exp. Med. 209, 1655–1670 (2012).

    CAS  PubMed Central  PubMed  Google Scholar 

  130. Myers, D. R., Zikherman, J. & Roose, J. P. Tonic signals: why do lymphocytes bother? Trends Immunol. 38, 844–857 (2017).

    CAS  PubMed Central  PubMed  Google Scholar 

  131. Boyman, O., Letourneau, S., Krieg, C. & Sprent, J. Homeostatic proliferation and survival of naive and memory T cells. Eur. J. Immunol. 39, 2088–2094 (2009).

    CAS  PubMed  Google Scholar 

  132. Sprent, J. & Surh, C. D. Normal T cell homeostasis: the conversion of naive cells into memory-phenotype cells. Nat. Immunol. 12, 478–484 (2011).

    CAS  PubMed Central  PubMed  Google Scholar 

  133. Karginov, T. A., Menoret, A. & Vella, A. T. Optimal CD8+ T cell effector function requires costimulation-induced RNA-binding proteins that reprogram the transcript isoform landscape. Nat. Commun. 13, 3540 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  134. Hernandez, R., Poder, J., LaPorte, K. M. & Malek, T. R. Engineering IL-2 for immunotherapy of autoimmunity and cancer. Nat. Rev. Immunol. 22, 614–628 (2022).

    CAS  PubMed  Google Scholar 

  135. Rosetti, F., Madera-Salcedo, I. K., Rodriguez-Rodriguez, N. & Crispin, J. C. Regulation of activated T cell survival in rheumatic autoimmune diseases. Nat. Rev. Rheumatol. 18, 232–244 (2022).

    CAS  PubMed  Google Scholar 

  136. Ogilvie, R. L. et al. Tristetraprolin down-regulates IL-2 gene expression through AU-rich element-mediated mRNA decay. J. Immunol. 174, 953–961 (2005).

    CAS  PubMed  Google Scholar 

  137. Salerno, F. et al. Translational repression of pre-formed cytokine-encoding mRNA prevents chronic activation of memory T cells. Nat. Immunol. 19, 828–837 (2018).

    CAS  PubMed Central  PubMed  Google Scholar 

  138. Ogilvie, R. L. et al. Tristetraprolin mediates interferon-γ mRNA decay. J. Biol. Chem. 284, 11216–11223 (2009).

    CAS  PubMed Central  PubMed  Google Scholar 

  139. Cook, M. E. et al. The ZFP36 family of RNA binding proteins regulates homeostatic and autoreactive T cell responses. Sci. Immunol. 7, eabo0981 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  140. Techasintana, P. et al. The RNA-binding protein HuR posttranscriptionally regulates IL-2 homeostasis and CD4+ Th2 differentiation. Immunohorizons 1, 109–123 (2017).

    CAS  PubMed Central  PubMed  Google Scholar 

  141. Petkau, G. et al. The timing of differentiation and potency of CD8 effector function is set by RNA binding proteins. Nat. Commun. 13, 2274 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  142. Zhou, J. et al. m6A demethylase ALKBH5 controls CD4+ T cell pathogenicity and promotes autoimmunity. Sci. Adv. https://doi.org/10.1126/sciadv.abg0470 (2021).

    Article  PubMed Central  PubMed  Google Scholar 

  143. Chen, J. et al. Posttranscriptional gene regulation of IL-17 by the RNA-binding protein HuR is required for initiation of experimental autoimmune encephalomyelitis. J. Immunol. 191, 5441–5450 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  144. Bluml, S. et al. Essential role of microRNA-155 in the pathogenesis of autoimmune arthritis in mice. Arthritis Rheum. 63, 1281–1288 (2011).

    PubMed  Google Scholar 

  145. Escobar, T., Yu, C. R., Muljo, S. A. & Egwuagu, C. E. STAT3 activates miR-155 in Th17 cells and acts in concert to promote experimental autoimmune uveitis. Invest. Ophthalmol. Vis. Sci. 54, 4017–4025 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  146. Murugaiyan, G., Beynon, V., Mittal, A., Joller, N. & Weiner, H. L. Silencing microRNA-155 ameliorates experimental autoimmune encephalomyelitis. J. Immunol. 187, 2213–2221 (2011).

    CAS  PubMed  Google Scholar 

  147. Escobar, T. M. et al. miR-155 activates cytokine gene expression in Th17 cells by regulating the DNA-binding protein Jarid2 to relieve polycomb-mediated repression. Immunity 40, 865–879 (2014).

    CAS  PubMed Central  PubMed  Google Scholar 

  148. Krebs, C. F. et al. MicroRNA-155 drives TH17 immune response and tissue injury in experimental crescentic GN. J. Am. Soc. Nephrol. 24, 1955–1965 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  149. Wang, H. et al. Negative regulation of Hif1a expression and TH17 differentiation by the hypoxia-regulated microRNA miR-210. Nat. Immunol. 15, 393–401 (2014).

    CAS  PubMed Central  PubMed  Google Scholar 

  150. Nyati, K. K., Zaman, M. M., Sharma, P. & Kishimoto, T. Arid5a, an RNA-binding protein in immune regulation: RNA stability, inflammation, and autoimmunity. Trends Immunol. 41, 255–268 (2020).

    CAS  PubMed  Google Scholar 

  151. Hanieh, H. et al. Arid5a stabilizes OX40 mRNA in murine CD4+ T cells by recognizing a stem-loop structure in its 3’UTR. Eur. J. Immunol. 48, 593–604 (2018).

    CAS  PubMed  Google Scholar 

  152. Croft, M. Control of immunity by the TNFR-related molecule OX40 (CD134). Annu. Rev. Immunol. 28, 57–78 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  153. Edner, N. M., Carlesso, G., Rush, J. S. & Walker, L. S. K. Targeting co-stimulatory molecules in autoimmune disease. Nat. Rev. Drug Discov. 19, 860–883 (2020).

    CAS  PubMed  Google Scholar 

  154. Masuda, K. et al. Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA. J. Exp. Med. 213, 605–619 (2016).

    CAS  PubMed Central  PubMed  Google Scholar 

  155. Masuda, K. et al. Arid5a controls IL-6 mRNA stability, which contributes to elevation of IL-6 level in vivo. Proc. Natl Acad. Sci. USA 110, 9409–9414 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  156. Taylor, T. C. et al. Arid5a mediates an IL-17-dependent pathway that drives autoimmunity but not antifungal host defense. J. Immunol. https://doi.org/10.4049/jimmunol.2200132 (2022).

    Article  PubMed  Google Scholar 

  157. Miao, R. et al. Targeted disruption of MCPIP1/Zc3h12a results in fatal inflammatory disease. Immunol. Cell Biol. 91, 368–376 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  158. Ansa-Addo, E. A. et al. RNA binding protein PCBP1 is an intracellular immune checkpoint for shaping T cell responses in cancer immunity. Sci. Adv. 6, eaaz3865 (2020).

    CAS  PubMed Central  PubMed  Google Scholar 

  159. Durant, L. et al. Diverse targets of the transcription factor STAT3 contribute to T cell pathogenicity and homeostasis. Immunity 32, 605–615 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  160. Zhou, L. et al. IL-6 programs TH-17 cell differentiation by promoting sequential engagement of the IL-21 and IL-23 pathways. Nat. Immunol. 8, 967–974 (2007).

    CAS  PubMed  Google Scholar 

  161. Ciofani, M. et al. A validated regulatory network for Th17 cell specification. Cell 151, 289–303 (2012).

    CAS  PubMed Central  PubMed  Google Scholar 

  162. Yoshimura, A., Naka, T. & Kubo, M. SOCS proteins, cytokine signalling and immune regulation. Nat. Rev. Immunol. 7, 454–465 (2007).

    CAS  PubMed  Google Scholar 

  163. Li, H. B. et al. m6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature 548, 338–342 (2017).

    CAS  PubMed Central  PubMed  Google Scholar 

  164. Liu, Y. et al. tRNA-m1A modification promotes T cell expansion via efficient MYC protein synthesis. Nat. Immunol. 23, 1433–1444 (2022).

    CAS  PubMed  Google Scholar 

  165. Bahrami, S. & Drablos, F. Gene regulation in the immediate-early response process. Adv. Biol. Regul. 62, 37–49 (2016).

    CAS  PubMed  Google Scholar 

  166. Lu, L. F. et al. Foxp3-dependent microRNA155 confers competitive fitness to regulatory T cells by targeting SOCS1 protein. Immunity 30, 80–91 (2009).

    CAS  PubMed Central  PubMed  Google Scholar 

  167. Dudda, J. C. et al. MicroRNA-155 is required for effector CD8+ T cell responses to virus infection and cancer. Immunity 38, 742–753 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  168. Schett, G. & Neurath, M. F. Resolution of chronic inflammatory disease: universal and tissue-specific concepts. Nat. Commun. 9, 3261 (2018).

    PubMed Central  PubMed  Google Scholar 

  169. Morell, M., Varela, N. & Maranon, C. Myeloid populations in systemic autoimmune diseases. Clin. Rev. Allergy Immunol. 53, 198–218 (2017).

    CAS  PubMed  Google Scholar 

  170. Psarras, A., Wittmann, M. & Vital, E. M. Emerging concepts of type I interferons in SLE pathogenesis and therapy. Nat. Rev. Rheumatol. 18, 575–590 (2022).

    CAS  PubMed  Google Scholar 

  171. Kurowska-Stolarska, M. & Alivernini, S. Synovial tissue macrophages in joint homeostasis, rheumatoid arthritis and disease remission. Nat. Rev. Rheumatol. 18, 384–397 (2022).

    CAS  PubMed  Google Scholar 

  172. Kopf, M., Bachmann, M. F. & Marsland, B. J. Averting inflammation by targeting the cytokine environment. Nat. Rev. Drug Discov. 9, 703–718 (2010).

    CAS  PubMed  Google Scholar 

  173. Burmester, G. R., Feist, E. & Dorner, T. Emerging cell and cytokine targets in rheumatoid arthritis. Nat. Rev. Rheumatol. 10, 77–88 (2014).

    CAS  PubMed  Google Scholar 

  174. McInnes, I. B., Buckley, C. D. & Isaacs, J. D. Cytokines in rheumatoid arthritis — shaping the immunological landscape. Nat. Rev. Rheumatol. 12, 63–68 (2016).

    CAS  PubMed  Google Scholar 

  175. McGeachy, M. J., Cua, D. J. & Gaffen, S. L. The IL-17 family of cytokines in health and disease. Immunity 50, 892–906 (2019).

    CAS  PubMed Central  Google Scholar 

  176. Ostareck, D. H. & Ostareck-Lederer, A. RNA-binding proteins in the control of LPS-induced macrophage response. Front. Genet. 10, 31 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  177. Liepelt, A. et al. Identification of RNA-binding proteins in macrophages by interactome capture. Mol. Cell Proteom. 15, 2699–2714 (2016).

    CAS  Google Scholar 

  178. Tiedje, C. et al. The RNA-binding protein TTP is a global post-transcriptional regulator of feedback control in inflammation. Nucleic Acids Res. 44, 7418–7440 (2016).

    CAS  PubMed Central  PubMed  Google Scholar 

  179. Shah, S., Mostafa, M. M., McWhae, A., Traves, S. L. & Newton, R. Negative feed-forward control of tumor necrosis factor (TNF) by tristetraprolin (ZFP36) is limited by the mitogen-activated protein kinase phosphatase, dual-specificity phosphatase 1 (DUSP1): implications for regulation by glucocorticoids. J. Biol. Chem. 291, 110–125 (2016).

    CAS  PubMed  Google Scholar 

  180. Molle, C. et al. Tristetraprolin regulation of interleukin 23 mRNA stability prevents a spontaneous inflammatory disease. J. Exp. Med. 210, 1675–1684 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  181. Chen, Y. L. et al. Transcriptional regulation of tristetraprolin by NF-κB signaling in LPS-stimulated macrophages. Mol. Biol. Rep. 40, 2867–2877 (2013).

    CAS  PubMed  Google Scholar 

  182. Carballo, E., Lai, W. S. & Blackshear, P. J. Evidence that tristetraprolin is a physiological regulator of granulocyte-macrophage colony-stimulating factor messenger RNA deadenylation and stability. Blood 95, 1891–1899 (2000).

    CAS  PubMed  Google Scholar 

  183. Carballo, E., Lai, W. S. & Blackshear, P. J. Feedback inhibition of macrophage tumor necrosis factor-α production by tristetraprolin. Science 281, 1001–1005 (1998).

    CAS  PubMed  Google Scholar 

  184. Taylor, G. A. et al. A pathogenetic role for TNF α in the syndrome of cachexia, arthritis, and autoimmunity resulting from tristetraprolin (TTP) deficiency. Immunity 4, 445–454 (1996).

    CAS  PubMed  Google Scholar 

  185. White, E. J., Brewer, G. & Wilson, G. M. Post-transcriptional control of gene expression by AUF1: mechanisms, physiological targets, and regulation. Biochim. Biophys. Acta 1829, 680–688 (2013).

    CAS  PubMed  Google Scholar 

  186. Lu, J. Y., Sadri, N. & Schneider, R. J. Endotoxic shock in AUF1 knockout mice mediated by failure to degrade proinflammatory cytokine mRNAs. Genes Dev. 20, 3174–3184 (2006).

    CAS  PubMed Central  PubMed  Google Scholar 

  187. Sadri, N. & Schneider, R. J. Auf1/Hnrnpd-deficient mice develop pruritic inflammatory skin disease. J. Invest. Dermatol. 129, 657–670 (2009).

    CAS  PubMed  Google Scholar 

  188. Czepielewski, R. S. et al. Ileitis-associated tertiary lymphoid organs arise at lymphatic valves and impede mesenteric lymph flow in response to tumor necrosis factor. Immunity 54, 2795–2811.e2799 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  189. Kontoyiannis, D., Pasparakis, M., Pizarro, T. T., Cominelli, F. & Kollias, G. Impaired on/off regulation of TNF biosynthesis in mice lacking TNF AU-rich elements: implications for joint and gut-associated immunopathologies. Immunity 10, 387–398 (1999).

    CAS  PubMed  Google Scholar 

  190. Kontoyiannis, D. et al. Genetic dissection of the cellular pathways and signaling mechanisms in modeled tumor necrosis factor-induced Crohn’s-like inflammatory bowel disease. J. Exp. Med. 196, 1563–1574 (2002).

    CAS  PubMed Central  PubMed  Google Scholar 

  191. Mino, T. et al. Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms. Cell 161, 1058–1073 (2015).

    CAS  PubMed  Google Scholar 

  192. Amatya, N. et al. IL-17 integrates multiple self-reinforcing, feed-forward mechanisms through the RNA binding protein Arid5a. Sci. Signal. https://doi.org/10.1126/scisignal.aat4617 (2018).

    Article  PubMed Central  PubMed  Google Scholar 

  193. Garg, A. V. et al. MCPIP1 endoribonuclease activity negatively regulates interleukin-17-mediated signaling and inflammation. Immunity 43, 475–487 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  194. Liu, B. et al. The RNase MCPIP3 promotes skin inflammation by orchestrating myeloid cytokine response. Nat. Commun. 12, 4105 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  195. O’Connell, R. M., Zhao, J. L. & Rao, D. S. MicroRNA function in myeloid biology. Blood 118, 2960–2969 (2011).

    PubMed Central  PubMed  Google Scholar 

  196. Tili, E. et al. Modulation of miR-155 and miR-125b levels following lipopolysaccharide/TNF-α stimulation and their possible roles in regulating the response to endotoxin shock. J. Immunol. 179, 5082–5089 (2007).

    CAS  PubMed  Google Scholar 

  197. Faraoni, I., Antonetti, F. R., Cardone, J. & Bonmassar, E. miR-155 gene: a typical multifunctional microRNA. Biochim. Biophys. Acta 1792, 497–505 (2009).

    CAS  PubMed  Google Scholar 

  198. Paoletti, A. et al. Monocyte/macrophage abnormalities specific to rheumatoid arthritis are linked to miR-155 and are differentially modulated by different TNF inhibitors. J. Immunol. 203, 1766–1775 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  199. Paoletti, A. et al. Restoration of default blood monocyte-derived macrophage polarization with adalimumab but not etanercept in rheumatoid arthritis. Front. Immunol. 13, 832117 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  200. Semaan, N. et al. miR-346 controls release of TNF-α protein and stability of its mRNA in rheumatoid arthritis via tristetraprolin stabilization. PLoS One 6, e19827 (2011).

    CAS  PubMed Central  PubMed  Google Scholar 

  201. Perez-Sanchez, C. et al. miR-374a-5p regulates inflammatory genes and monocyte function in patients with inflammatory bowel disease. J. Exp. Med. 9, https://doi.org/10.1084/jem.20211366 (2022).

  202. Taganov, K. D., Boldin, M. P., Chang, K. J. & Baltimore, D. NF-κB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc. Natl Acad. Sci. USA 103, 12481–12486 (2006).

    CAS  PubMed Central  PubMed  Google Scholar 

  203. von Gamm, M. et al. Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3. J. Exp. Med. 216, 1700–1723 (2019).

    Google Scholar 

  204. Winkler, R. et al. m6A modification controls the innate immune response to infection by targeting type I interferons. Nat. Immunol. 20, 173–182 (2019).

    CAS  PubMed  Google Scholar 

  205. McFadden, M. J. & Horner, S. M. N6-methyladenosine regulates host responses to viral infection. Trends Biochem. Sci. 46, 366–377 (2021).

    CAS  PubMed  Google Scholar 

  206. Banchereau, J. & Pascual, V. Type I interferon in systemic lupus erythematosus and other autoimmune diseases. Immunity 25, 383–392 (2006).

    CAS  PubMed  Google Scholar 

  207. Wang, H. et al. Mettl3-mediated mRNA m6A methylation promotes dendritic cell activation. Nat. Commun. 10, 1898 (2019).

    PubMed Central  PubMed  Google Scholar 

  208. Han, D. et al. Anti-tumour immunity controlled through mRNA m6A methylation and YTHDF1 in dendritic cells. Nature 566, 270–274 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  209. Aeschlimann, F. A. et al. A20 haploinsufficiency (HA20): clinical phenotypes and disease course of patients with a newly recognised NF-kB-mediated autoinflammatory disease. Ann. Rheum. Dis. 77, 728–735 (2018).

    CAS  PubMed  Google Scholar 

  210. Tak, P. P. & Firestein, G. S. NF-κB: a key role in inflammatory diseases. J. Clin. Invest. 107, 7–11 (2001).

    CAS  PubMed Central  PubMed  Google Scholar 

  211. Nocturne, G. et al. Germline and somatic genetic variations of TNFAIP3 in lymphoma complicating primary Sjögren’s syndrome. Blood 122, 4068–4076 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  212. Niu, J. et al. USP10 inhibits genotoxic NF-κB activation by MCPIP1-facilitated deubiquitination of NEMO. EMBO J. 32, 3206–3219 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  213. Perry, M. M. et al. Rapid changes in microRNA-146a expression negatively regulate the IL-1β-induced inflammatory response in human lung alveolar epithelial cells. J. Immunol. 180, 5689–5698 (2008).

    CAS  PubMed  Google Scholar 

  214. Zhu, S. et al. The microRNA miR-23b suppresses IL-17-associated autoimmune inflammation by targeting TAB2, TAB3 and IKK-α. Nat. Med. 18, 1077–1086 (2012).

    CAS  PubMed  Google Scholar 

  215. Prescott, J. A., Mitchell, J. P. & Cook, S. J. Inhibitory feedback control of NF-κB signalling in health and disease. Biochem. J. 478, 2619–2664 (2021).

    CAS  PubMed  Google Scholar 

  216. Skalniak, L. et al. Regulatory feedback loop between NF-κB and MCP-1-induced protein 1 RNase. FEBS J. 276, 5892–5905 (2009).

    CAS  PubMed  Google Scholar 

  217. Schichl, Y. M., Resch, U., Hofer-Warbinek, R. & de Martin, R. Tristetraprolin impairs NF-κB/p65 nuclear translocation. J. Biol. Chem. 284, 29571–29581 (2009).

    CAS  PubMed Central  PubMed  Google Scholar 

  218. Zhang, W., Vreeland, A. C. & Noy, N. RNA-binding protein HuR regulates nuclear import of protein. J. Cell Sci. 129, 4025–4033 (2016).

    CAS  PubMed Central  PubMed  Google Scholar 

  219. Gantier, M. P. et al. A miR-19 regulon that controls NF-κB signaling. Nucleic Acids Res. 40, 8048–8058 (2012).

    CAS  PubMed Central  PubMed  Google Scholar 

  220. Marshak-Rothstein, A. Toll-like receptors in systemic autoimmune disease. Nat. Rev. Immunol. 6, 823–835 (2006).

    CAS  PubMed Central  PubMed  Google Scholar 

  221. Wells, C. A. et al. Alternate transcription of the Toll-like receptor signaling cascade. Genome Biol. 7, R10 (2006).

    PubMed Central  PubMed  Google Scholar 

  222. Noack, M. & Miossec, P. Importance of lymphocyte-stromal cell interactions in autoimmune and inflammatory rheumatic diseases. Nat. Rev. Rheumatol. 17, 550–564 (2021).

    CAS  PubMed  Google Scholar 

  223. Buckley, C. D., Ospelt, C., Gay, S. & Midwood, K. S. Location, location, location: how the tissue microenvironment affects inflammation in RA. Nat. Rev. Rheumatol. 17, 195–212 (2021).

    PubMed  Google Scholar 

  224. Riviere, E. et al. Interleukin-7/interferon axis drives T cell and salivary gland epithelial cell interactions in Sjögren’s syndrome. Arthritis Rheumatol. 73, 631–640 (2021).

    CAS  PubMed  Google Scholar 

  225. Verstappen, G. M., Pringle, S., Bootsma, H. & Kroese, F. G. M. Epithelial–immune cell interplay in primary Sjögren syndrome salivary gland pathogenesis. Nat. Rev. Rheumatol. 17, 333–348 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  226. Nowarski, R., Jackson, R. & Flavell, R. A. The stromal intervention: regulation of immunity and inflammation at the epithelial-mesenchymal barrier. Cell 168, 362–375 (2017).

    CAS  PubMed  Google Scholar 

  227. Riviere, E. et al. Salivary gland epithelial cells from patients with Sjögren’s syndrome induce B-lymphocyte survival and activation. Ann. Rheum. Dis. 79, 1468–1477 (2020).

    CAS  PubMed  Google Scholar 

  228. Angiolilli, C. et al. ZFP36 family members regulate the proinflammatory features of psoriatic dermal fibroblasts. J. Invest. Dermatol. 142, 402–413 (2022).

    CAS  PubMed  Google Scholar 

  229. Koliaraki, V., Prados, A., Armaka, M. & Kollias, G. The mesenchymal context in inflammation, immunity and cancer. Nat. Immunol. https://doi.org/10.1038/s41590-020-0741-2 (2020).

    Article  PubMed  Google Scholar 

  230. Krausgruber, T. et al. Structural cells are key regulators of organ-specific immune responses. Nature 583, 296–302 (2020).

    CAS  PubMed Central  PubMed  Google Scholar 

  231. Nygaard, G. & Firestein, G. S. Restoring synovial homeostasis in rheumatoid arthritis by targeting fibroblast-like synoviocytes. Nat. Rev. Rheumatol. https://doi.org/10.1038/s41584-020-0413-5 (2020).

    Article  PubMed Central  PubMed  Google Scholar 

  232. Dasoveanu, D. C. et al. Lymph node stromal CCL2 limits antibody responses. Sci. Immunol. https://doi.org/10.1126/sciimmunol.aaw0693 (2020).

    Article  PubMed Central  PubMed  Google Scholar 

  233. Martin, E. W., Pacholewska, A., Patel, H., Dashora, H. & Sung, M. H. Integrative analysis suggests cell type-specific decoding of NF-κB dynamics. Sci. Signal. https://doi.org/10.1126/scisignal.aax7195 (2020).

    Article  PubMed Central  PubMed  Google Scholar 

  234. Bordon, Y. Stromal support from IL-17. Nat. Rev. Immunol. 19, 270–271 (2019).

    PubMed  Google Scholar 

  235. de Oliveira, P. G., Farinon, M., Sanchez-Lopez, E., Miyamoto, S. & Guma, M. Fibroblast-like synoviocytes glucose metabolism as a therapeutic target in rheumatoid arthritis. Front. Immunol. 10, 1743 (2019).

    PubMed Central  PubMed  Google Scholar 

  236. Saeki, N. et al. Epigenetic regulator UHRF1 orchestrates proinflammatory gene expression in rheumatoid arthritis in a suppressive manner. J. Clin. Invest. https://doi.org/10.1172/JCI150533 (2022).

    Article  PubMed Central  PubMed  Google Scholar 

  237. Gall, A. et al. Autoimmunity initiates in nonhematopoietic cells and progresses via lymphocytes in an interferon-dependent autoimmune disease. Immunity 36, 120–131 (2012).

    CAS  PubMed Central  PubMed  Google Scholar 

  238. Koliaraki, V., Dotto, G. P., Buckley, C. D. & Kollias, G. Mesenchymal cells in health and disease. Nat. Immunol. 23, 1395–1398 (2022).

    CAS  PubMed  Google Scholar 

  239. Li, X., Bechara, R., Zhao, J., McGeachy, M. J. & Gaffen, S. L. IL-17 receptor-based signaling and implications for disease. Nat. Immunol. 20, 1594–1602 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  240. Bechara, R., McGeachy, M. J. & Gaffen, S. L. The metabolism-modulating activity of IL-17 signaling in health and disease. J. Exp. Med. https://doi.org/10.1084/jem.20202191 (2021).

    Article  PubMed Central  PubMed  Google Scholar 

  241. Monin, L. et al. MCPIP1/Regnase-1 restricts IL-17A- and IL-17C-dependent skin inflammation. J. Immunol. 198, 767–775 (2017).

    CAS  PubMed  Google Scholar 

  242. Li, D. D. et al. RTEC-intrinsic IL-17-driven inflammatory circuit amplifies antibody-induced glomerulonephritis and is constrained by Regnase-1. JCI Insight https://doi.org/10.1172/jci.insight.147505 (2021).

    Article  PubMed Central  PubMed  Google Scholar 

  243. Herjan, T. et al. IL-17-receptor-associated adaptor Act1 directly stabilizes mRNAs to mediate IL-17 inflammatory signaling. Nat. Immunol. 19, 354–365 (2018).

    CAS  PubMed Central  PubMed  Google Scholar 

  244. Herjan, T. et al. HuR is required for IL-17-induced Act1-mediated CXCL1 and CXCL5 mRNA stabilization. J. Immunol. 191, 640–649 (2013).

    CAS  PubMed  Google Scholar 

  245. Bechara, R. et al. The m6A reader IMP2 directs autoimmune inflammation through an IL-17- and TNFα-dependent C/EBP transcription factor axis. Sci. Immunol. https://doi.org/10.1126/sciimmunol.abd1287 (2021).

    Article  PubMed Central  PubMed  Google Scholar 

  246. Bechara, R. et al. The RNA-binding protein IMP2 drives a stromal-Th17 cell circuit in autoimmune neuroinflammation. JCI Insight https://doi.org/10.1172/jci.insight.152766 (2022).

    Article  PubMed Central  PubMed  Google Scholar 

  247. Mueller, S. N. IL-17 instructs lymphoid stromal cells. Nat. Immunol. 20, 524–526 (2019).

    CAS  PubMed  Google Scholar 

  248. Majumder, S. et al. IL-17 metabolically reprograms activated fibroblastic reticular cells for proliferation and survival. Nat. Immunol. 20, 534–545 (2019).

    CAS  PubMed Central  Google Scholar 

  249. Qiu, L. Q., Stumpo, D. J. & Blackshear, P. J. Myeloid-specific tristetraprolin deficiency in mice results in extreme lipopolysaccharide sensitivity in an otherwise minimal phenotype. J. Immunol. 188, 5150–5159 (2012).

    CAS  PubMed  Google Scholar 

  250. Andrianne, M. et al. Tristetraprolin expression by keratinocytes controls local and systemic inflammation. JCI Insight https://doi.org/10.1172/jci.insight.92979 (2017).

    Article  PubMed Central  PubMed  Google Scholar 

  251. Liu, L. et al. Zc3h12c inhibits vascular inflammation by repressing NF-κB activation and pro-inflammatory gene expression in endothelial cells. Biochem. J. 451, 55–60 (2013).

    CAS  PubMed  Google Scholar 

  252. Wan, Q., Zhou, Z., Ding, S. & He, J. The miR-30a negatively regulates IL-17-mediated signal transduction by targeting Traf3ip2. J. Interferon Cytokine Res. 35, 917–923 (2015).

    CAS  PubMed  Google Scholar 

  253. Dhuppar, S. & Murugaiyan, G. miRNA effects on gut homeostasis: therapeutic implications for inflammatory bowel disease. Trends Immunol. https://doi.org/10.1016/j.it.2022.09.003 (2022).

    Article  PubMed  Google Scholar 

  254. Jimenez, M. T. et al. The miR-181 family regulates colonic inflammation through its activity in the intestinal epithelium. J. Exp. Med. https://doi.org/10.1084/jem.20212278 (2022).

    Article  PubMed Central  PubMed  Google Scholar 

  255. Junker, A. et al. MicroRNA profiling of multiple sclerosis lesions identifies modulators of the regulatory protein CD47. Brain 132, 3342–3352 (2009).

    PubMed  Google Scholar 

  256. Stanczyk, J. et al. Altered expression of microRNA in synovial fibroblasts and synovial tissue in rheumatoid arthritis. Arthritis Rheum. 58, 1001–1009 (2008).

    PubMed  Google Scholar 

  257. Saito, Y. et al. AT-rich-interactive domain-containing protein 5A functions as a negative regulator of retinoic acid receptor-related orphan nuclear receptor γt-induced Th17 cell differentiation. Arthritis Rheumatol. 66, 1185–1194 (2014).

    CAS  PubMed  Google Scholar 

  258. Cook, C. P. et al. A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity. Cell Rep. Med. 3, 100715 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  259. Tsutsumi, A. et al. Expression of tristetraprolin (G0S24) mRNA, a regulator of tumor necrosis factor-alpha production, in synovial tissues of patients with rheumatoid arthritis. J. Rheumatol. 31, 1044–1049 (2004).

    CAS  PubMed  Google Scholar 

  260. Ross, E. A. et al. Treatment of inflammatory arthritis via targeting of tristetraprolin, a master regulator of pro-inflammatory gene expression. Ann. Rheum. Dis. 76, 612–619 (2017).

    CAS  PubMed  Google Scholar 

  261. Di Silvestre, A. et al. Role of tristetraprolin phosphorylation in paediatric patients with inflammatory bowel disease. World J. Gastroenterol. 25, 5918–5925 (2019).

    PubMed Central  PubMed  Google Scholar 

  262. Castello, A. et al. Comprehensive identification of RNA-binding domains in human cells. Mol. Cell 63, 696–710 (2016).

    CAS  PubMed Central  PubMed  Google Scholar 

  263. Tavernier, S. J. et al. A human immune dysregulation syndrome characterized by severe hyperinflammation with a homozygous nonsense Roquin-1 mutation. Nat. Commun. 10, 4779 (2019).

    CAS  PubMed Central  PubMed  Google Scholar 

  264. Tsoi, L. C. et al. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat. Genet. 44, 1341–1348 (2012).

    CAS  PubMed Central  PubMed  Google Scholar 

  265. Carrick, D. M. et al. Genetic variations in ZFP36 and their possible relationship to autoimmune diseases. J. Autoimmun. 26, 182–196 (2006).

    CAS  PubMed  Google Scholar 

  266. Hinks, A. et al. Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis. Nat. Genet. 45, 664–669 (2013).

    CAS  PubMed Central  PubMed  Google Scholar 

  267. Franke, A. et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci. Nat. Genet. 42, 1118–1125 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  268. International Multiple Sclerosis Genetics, C. Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. Science https://doi.org/10.1126/science.aav7188 (2019).

    Article  Google Scholar 

  269. Skriner, K. et al. AUF1, the regulator of tumor necrosis factor α messenger RNA decay, is targeted by autoantibodies of patients with systemic rheumatic diseases. Arthritis Rheum. 58, 511–520 (2008).

    CAS  PubMed  Google Scholar 

  270. Hung, T. et al. The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. Science 350, 455–459 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  271. Clark, G., Reichlin, M. & Tomasi, T. B. Jr. Characterization of a soluble cytoplasmic antigen reactive with sera from patients with systemic lupus erythematosus. J. Immunol. 102, 117–122 (1969).

    CAS  PubMed  Google Scholar 

  272. Alspaugh, M. & Maddison, P. Resolution of the identity of certain antigen–antibody systems in systemic lupus erythematosus and Sjögren’s syndrome: an interlaboratory collaboration. Arthritis Rheum. 22, 796–798 (1979).

    CAS  PubMed  Google Scholar 

  273. Soret, P. et al. A new molecular classification to drive precision treatment strategies in primary Sjögren’s syndrome. Nat. Commun. 12, 3523 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  274. Kirou, K. A. et al. Activation of the interferon-α pathway identifies a subgroup of systemic lupus erythematosus patients with distinct serologic features and active disease. Arthritis Rheum. 52, 1491–1503 (2005).

    CAS  PubMed  Google Scholar 

  275. Baechler, E. C. et al. Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc. Natl Acad. Sci. USA 100, 2610–2615 (2003).

    CAS  PubMed Central  PubMed  Google Scholar 

  276. Mariette, X. et al. The level of BLyS (BAFF) correlates with the titre of autoantibodies in human Sjögren’s syndrome. Ann. Rheum. Dis. 62, 168–171 (2003).

    CAS  PubMed Central  PubMed  Google Scholar 

  277. Maraia, R. J., Sasaki-Tozawa, N., Driscoll, C. T., Green, E. D. & Darlington, G. J. The human Y4 small cytoplasmic RNA gene is controlled by upstream elements and resides on chromosome 7 with all other hY scRNA genes. Nucleic Acids Res. 22, 3045–3052 (1994).

    CAS  PubMed Central  PubMed  Google Scholar 

  278. Schlee, M. & Hartmann, G. Discriminating self from non-self in nucleic acid sensing. Nat. Rev. Immunol. 16, 566–580 (2016).

    CAS  PubMed Central  PubMed  Google Scholar 

  279. Devarkar, S. C. et al. Structural basis for m7G recognition and 2’-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc. Natl Acad. Sci. USA 113, 596–601 (2016).

    CAS  PubMed Central  PubMed  Google Scholar 

  280. Despic, V. & Jaffrey, S. R. mRNA ageing shapes the Cap2 methylome in mammalian mRNA. Nature 614, 358–366 (2023).

    CAS  PubMed Central  PubMed  Google Scholar 

  281. Zust, R. et al. Ribose 2’-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5. Nat. Immunol. 12, 137–143 (2011).

    PubMed Central  PubMed  Google Scholar 

  282. Hubbard, N. W. et al. ADAR1 mutation causes ZBP1-dependent immunopathology. Nature 607, 769–775 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  283. de Reuver, R. et al. ADAR1 prevents autoinflammation by suppressing spontaneous ZBP1 activation. Nature 607, 784–789 (2022).

    PubMed  Google Scholar 

  284. Jiao, H. et al. ADAR1 averts fatal type I interferon induction by ZBP1. Nature 607, 776–783 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  285. Liddicoat, B. J. et al. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science 349, 1115–1120 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  286. Pestal, K. et al. Isoforms of RNA-editing enzyme ADAR1 independently control nucleic acid sensor MDA5-driven autoimmunity and multi-organ development. Immunity 43, 933–944 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

  287. Rice, G. I. et al. Mutations in ADAR1 cause Aicardi-Goutieres syndrome associated with a type I interferon signature. Nat. Genet. 44, 1243–1248 (2012).

    CAS  PubMed Central  PubMed  Google Scholar 

  288. Wolf, C. & Lee-Kirsch, M. A. Keeping immunostimulatory self-RNA under the rADAR. Nat. Rev. Rheumatol. https://doi.org/10.1038/s41584-022-00859-4 (2022).

    Article  PubMed  Google Scholar 

  289. Roberts, T. C., Langer, R. & Wood, M. J. A. Advances in oligonucleotide drug delivery. Nat. Rev. Drug Discov. 19, 673–694 (2020).

    CAS  PubMed Central  PubMed  Google Scholar 

  290. Crooke, S. T., Witztum, J. L., Bennett, C. F. & Baker, B. F. RNA-targeted therapeutics. Cell Metab. 27, 714–739 (2018).

    CAS  PubMed  Google Scholar 

  291. Rupaimoole, R. & Slack, F. J. MicroRNA therapeutics: towards a new era for the management of cancer and other diseases. Nat. Rev. Drug Discov. 16, 203–222 (2017).

    CAS  PubMed  Google Scholar 

  292. Garber, K. mRNA pioneers refocus on therapeutics. Nat. Rev. Drug Discov. 21, 699–701 (2022).

    CAS  PubMed  Google Scholar 

  293. Childs-Disney, J. L. et al. Targeting RNA structures with small molecules. Nat. Rev. Drug Discov. 21, 736–762 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  294. Mino, T. & Takeuchi, O. Regnase-1-related endoribonucleases in health and immunological diseases. Immunol. Rev. 304, 97–110 (2021).

    CAS  PubMed  Google Scholar 

  295. Yankova, E. et al. Small molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature https://doi.org/10.1038/s41586-021-03536-w (2021).

    Article  PubMed Central  PubMed  Google Scholar 

  296. Masuda, K. & Kishimoto, T. A potential therapeutic target RNA-binding protein, Arid5a for the treatment of inflammatory disease associated with aberrant cytokine expression. Curr. Pharm. Des. 24, 1766–1771 (2018).

    CAS  PubMed  Google Scholar 

  297. Hoefig, K. P. et al. Defining the RBPome of primary T helper cells to elucidate higher-order Roquin-mediated mRNA regulation. Nat. Commun. 12, 5208 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  298. Keene, J. D. RNA regulons: coordination of post-transcriptional events. Nat. Rev. Genet. 8, 533–543 (2007).

    CAS  PubMed  Google Scholar 

  299. Xiao, Y. L. et al. Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination. Nat. Biotechnol. https://doi.org/10.1038/s41587-022-01587-6 (2023).

    Article  PubMed  Google Scholar 

  300. Sun, W. et al. Genetically encoded chemical crosslinking of RNA in vivo. Nat. Chem. https://doi.org/10.1038/s41557-022-01038-4 (2022).

    Article  PubMed Central  PubMed  Google Scholar 

  301. Tegowski, M., Flamand, M. N. & Meyer, K. D. scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells. Mol. Cell 82, 868–878 e810 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  302. Zhao, Z., Ukidve, A., Kim, J. & Mitragotri, S. Targeting strategies for tissue-specific drug delivery. Cell 181, 151–167 (2020).

    CAS  PubMed  Google Scholar 

  303. Mukherjee, N. et al. Global target mRNA specification and regulation by the RNA-binding protein ZFP36. Genome Biol. 15, R12 (2014).

    PubMed Central  PubMed  Google Scholar 

  304. Chen, J. et al. The RNA-binding protein HuR contributes to neuroinflammation by promoting C-C chemokine receptor 6 (CCR6) expression on Th17 cells. J. Biol. Chem. 292, 14532–14543 (2017).

    CAS  PubMed Central  PubMed  Google Scholar 

  305. Du, C. et al. MicroRNA miR-326 regulates TH-17 differentiation and is associated with the pathogenesis of multiple sclerosis. Nat. Immunol. 10, 1252–1259 (2009).

    CAS  PubMed  Google Scholar 

  306. Kohlhaas, S. et al. Cutting edge: the Foxp3 target miR-155 contributes to the development of regulatory T cells. J. Immunol. 182, 2578–2582 (2009).

    CAS  PubMed  Google Scholar 

  307. O’Connell, R. M. et al. MicroRNA-155 promotes autoimmune inflammation by enhancing inflammatory T cell development. Immunity 33, 607–619 (2010).

    PubMed Central  PubMed  Google Scholar 

  308. Hu, R. et al. MicroRNA-155 confers encephalogenic potential to Th17 cells by promoting effector gene expression. J. Immunol. 190, 5972–5980 (2013).

    CAS  PubMed  Google Scholar 

  309. Lu, L. F. et al. Function of miR-146a in controlling Treg cell-mediated regulation of Th1 responses. Cell 142, 914–929 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  310. Boldin, M. P. et al. miR-146a is a significant brake on autoimmunity, myeloproliferation, and cancer in mice. J. Exp. Med. 208, 1189–1201 (2011).

    CAS  PubMed Central  PubMed  Google Scholar 

  311. He, P. C. et al. Exon architecture controls mRNA m6A suppression and gene expression. Science 379, 677–682 (2023).

    CAS  PubMed  Google Scholar 

  312. Uzonyi, A. et al. Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability. Mol. Cell 83, 237–251 e237 (2023).

    CAS  PubMed  Google Scholar 

  313. Thompson, M. G., Sacco, M. T. & Horner, S. M. How RNA modifications regulate the antiviral response. Immunol. Rev. https://doi.org/10.1111/imr.13020 (2021).

    Article  PubMed Central  PubMed  Google Scholar 

  314. Zheng, Q., Hou, J., Zhou, Y., Li, Z. & Cao, X. The RNA helicase DDX46 inhibits innate immunity by entrapping m6A-demethylated antiviral transcripts in the nucleus. Nat. Immunol. 18, 1094–1103 (2017).

    CAS  PubMed  Google Scholar 

  315. Kariko, K., Buckstein, M., Ni, H. & Weissman, D. Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA. Immunity 23, 165–175 (2005).

    CAS  PubMed  Google Scholar 

  316. Durbin, A. F., Wang, C., Marcotrigiano, J. & Gehrke, L. RNAs containing modified nucleotides fail to trigger RIG-I conformational changes for innate immune signaling. mBio https://doi.org/10.1128/mBio.00833-16 (2016).

    Article  PubMed Central  PubMed  Google Scholar 

  317. Luo, S. et al. METTL3-mediated m6A mRNA methylation regulates neutrophil activation through targeting TLR4 signaling. Cell Rep. 42, 112259 (2023).

    CAS  PubMed  Google Scholar 

  318. Song, H. et al. METTL3-mediated m6A RNA methylation promotes the anti-tumour immunity of natural killer cells. Nat. Commun. 12, 5522 (2021).

    CAS  PubMed Central  PubMed  Google Scholar 

  319. Ding, C. et al. RNA m6A demethylase ALKBH5 regulates the development of γδ T cells. Proc. Natl Acad. Sci. USA 119, e2203318119 (2022).

    CAS  PubMed Central  PubMed  Google Scholar 

  320. Cho, J. H. & Feldman, M. Heterogeneity of autoimmune diseases: pathophysiologic insights from genetics and implications for new therapies. Nat. Med. 21, 730–738 (2015).

    CAS  PubMed Central  PubMed  Google Scholar 

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Acknowledgements

This work has been supported as part of France 2030 program “ANR-11-IDEX-0003”, from the OI HEALTHI of the Université Paris-Saclay.

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Bechara, R., Vagner, S. & Mariette, X. Post-transcriptional checkpoints in autoimmunity. Nat Rev Rheumatol 19, 486–502 (2023). https://doi.org/10.1038/s41584-023-00980-y

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