1. P. Anderson, Post-transcriptional control of cytokine production. Nat. Immunol. 9, 353–359 (2008).
2. T. Glisovic, J. L. Bachorik, J. Yong, G. Dreyfuss, RNA-binding proteins and posttranscriptional gene regulation. FEBS Lett. 582, 1977–1986 (2008).
3. S. Carpenter, E. P. Ricci, B. C. Mercier, M. J. Moore, K. A. Fitzgerald, Post-transcriptional regulation of gene expression in innate immunity. Nat. Rev. Immunol. 14, 361–376 (2014).
4. K. Matsushita, O. Takeuchi, D. M. Standley, Y. Kumagai, T. Kawagoe, T. Miyake, T. Satoh, H. Kato, T. Tsujimura, H. Nakamura, S. Akira, Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Nature 458, 1185–1190 (2009).
5. H. Iwasaki, O. Takeuchi, S. Teraguchi, K. Matsushita, T. Uehata, K. Kuniyoshi, T. Satoh, T. Saitoh, M. Matsushita, D. M. Standley, S. Akira, The IB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1. Nat. Immunol. 12, 1167–1175 (2011).
6. T. Uehata, H. Iwasaki, A. Vandenbon, K. Matsushita, E. Hernandez-Cuellar, K. Kuniyoshi, T. Satoh, T. Mino, Y. Suzuki, D. M. Standley, T. Tsujimura, H. Rakugi, Y. Isaka, O. Takeuchi, S. Akira, Malt1-induced cleavage of regnase-1 in CD4(+) helper T cells regulates immune activation. Cell 153, 1036–1049 (2013).
7. T. Mino, Y. Murakawa, A. Fukao, A. Vandenbon, H. H. Wessels, D. Ori, T. Uehata, S. Tartey, S. Akira, Y. Suzuki, C. G. Vinuesa, U. Ohler, D. M. Standley, M. Landthaler, T. Fujiwara, O. Takeuchi, Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms. Cell 161, 1058–1073 (2015).
8. T. Mino, N. Iwai, M. Endo, K. Inoue, K. Akaki, F. Hia, T. Uehata, T. Emura, K. Hidaka, Y. Suzuki, D. M. Standley, M. Okada-Hatakeyama, S. Ohno, H. Sugiyama, A. Yamashita, O. Takeuchi, Translation-dependent unwinding ofstem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs. Nucleic Acids Res. 47, 8838–8859 (2019).
9. X. Cui, T. Mino, M. Yoshinaga, Y. Nakatsuka, F. Hia, D. Yamasoba, T. Tsujimura, K. Tomonaga, Y. Suzuki, T. Uehata, O. Takeuchi, Regnase-1 and roquin nonredundantly regulate Th1 differentiation causing cardiac inflammation and fibrosis. J. Immunol. 199, 4066–4077 (2017).
10. Y. Nakatsuka, A. Vandenbon, T. Mino, M. Yoshinaga, T. Uehata, X. Cui, A. Sato, T. Tsujimura, Y. Suzuki, A. Sato, T. Handa, K. Chin, T. Sawa, T. Hirai, O. Takeuchi, Pulmonary regnase-1 orchestrates the interplay of epithelium and adaptive immune systems to protect against pneumonia. Mucosal Immunol. 11, 1203–1218 (2018).
11. K. Nanki, M. Fujii, M. Shimokawa, M. Matano, S. Nishikori, S. Date, A. Takano, K. Toshimitsu, Y. Ohta, S. Takahashi, S. Sugimoto, K. Ishimaru, K. Kawasaki, Y. Nagai, R. Ishii, K. Yoshida, N. Sasaki, T. Hibi, S. Ishihara, T. Kanai, T. Sato, Somatic inflammatory gene mutations in human ulcerative colitis epithelium. Nature 577, 254–259 (2020).
12. N. Kakiuchi, K. Yoshida, M. Uchino, T. Kihara, K. Akaki, Y. Inoue, K. Kawada, S. Nagayama, A. Yokoyama, S. Yamamoto, M. Matsuura, T. Horimatsu, T. Hirano, N. Goto, Y. Takeuchi, Y. Ochi, Y. Shiozawa, Y. Kogure, Y. Watatani, Y. Fujii, S. K. Kim, A. Kon, K. Kataoka, T. Yoshizato, M. M. Nakagawa, A. Yoda, Y. Nanya, H. Makishima, Y. Shiraishi, K. Chiba, H. Tanaka, M. Sanada, E. Sugihara, T. A. Sato, T. Maruyama, H. Miyoshi, M. M. Taketo, J. Oishi, R. Inagaki, Y. Ueda, S. Okamoto, H. Okajima, Y. Sakai, T. Sakurai, H. Haga, S. Hirota, H. Ikeuchi, H. Nakase, H. Marusawa, T. Chiba, O. Takeuchi, S. Miyano, H. Seno, S. Ogawa, Frequent mutations that converge on the NFKBIZ pathway in ulcerative colitis. Nature 577, 260–265 (2020).
13. Y. Nakatsuka, A. Yaku, T. Handa, A. Vandenbon, Y. Hikichi, Y. Motomura, A. Sato, M. Yoshinaga, K. Tanizawa, K. Watanabe, T. Hirai, K. Chin, Y. Suzuki, T. Uehata, T. Mino, T. Tsujimura, K. Moro, O. Takeuchi, Profibrotic function of pulmonary group 2 innate lymphoid cells is controlled by regnase-1. Eur. Respir. J. 57, 2000018 (2021).
14. J. Wei, L. Long, W. Zheng, Y. Dhungana, S. A. Lim, C. Guy, Y. Wang, Y. D. Wang, C. Qian, B. Xu, A. Kc, J. Saravia, H. Huang, J. Yu, J. G. Doench, T. L. Geiger, H. Chi, Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy. Nature 576, 471–476 (2019).
15. N. Delihas, S. E. Rokita, P. Zheng, Natural antisense RNA/target RNA interactions: Possible models for antisense oligonucleotide drug design. Nat. Biotechnol. 15, 751–753 (1997).
16. W. Lima, H. Wu, S. T. Crooke, The RNase H mechanism, in Antisense Drug Technology: Principles, Strategies, and Applications (CRC Press, ed. Second Edition, 2007), pp. 65–92.
17. D. A. Melton, Injected anti-sense RNAs specifically block messenger RNA translation in vivo. Proc. Natl. Acad. Sci. U.S.A. 82, 144–148 (1985).
18. D. Hodges, S. T. Crooke, Inhibition ofsplicing of wild-type and mutated luciferaseadenovirus pre-mRNAs by antisense oligonucleotides. Mol. Pharmacol. 48, 905–918 (1995).
19. R. S. Finkel, E. Mercuri, B. T. Darras, A. M. Connolly, N. L. Kuntz, J. Kirschner, C. A. Chiriboga, K. Saito, L. Servais, E. Tizzano, H. Topaloglu, M. Tulinius, J. Montes, A. M. Glanzman, K. Bishop, Z. J. Zhong, S. Gheuens, C. F. Bennett, E. Schneider, W. Farwell, D. C. De Vivo, Nusinersen versus sham control in infantile-onset spinal muscular atrophy. N. Engl. J. Med. 377, 1723–1732 (2017).
20. J. S. Charleston, F. J. Schnell, J. Dworzak, C. Donoghue, S. Lewis, L. Chen, G. D. Young, A. J. Milici, J. Voss, U. DeAlwis, B. Wentworth, L. R. Rodino-Klapac, Z. Sahenk, D. Frank, J. R. Mendell, Eteplirsen treatment forDuchenne muscular dystrophy: Exon skipping and dystrophin production. Neurology 90, e2146–e2154 (2018).
21. U. A. Ørom, S. Kauppinen, A. H. Lund, LNA-modified oligonucleotides mediate specific inhibition of microRNA function. Gene 372, 137–141 (2006).
22. S. T. Crooke, X. H. Liang, R. M. Crooke, B. F. Baker, R. S. Geary, Antisense drug discovery and development technology considered in a pharmacological context. Biochem. Pharmacol. 189, 114196 (2021).
23. T. C. Roberts, R. Langer, M. J. A. Wood, Advances in oligonucleotide drug delivery. Nat. Rev. Drug Discov. 19, 673–694 (2020).
24. S. T. Crooke, B. F. Baker, R. M. Crooke, X. H. Liang, Antisense technology: An overview and prospectus. Nat. Rev. Drug Discov. 20, 427–453 (2021).
25. S. M. García-Mauriño, F. Rivero-Rodríguez, A. Velázquez-Cruz, M. Hernández-Vellisca, A. Díaz-Quintana, M. A. De la Rosa, I. Díaz-Moreno, RNA binding protein regulation and cross-talk in the control of AU-rich mRNA fate. Front. Mol. Biosci. 4, (2017).
26. P. A. Morcos, Y. Li, S. Jiang, Vivo-Morpholinos: A non-peptide transporter delivers Morpholinos into a wide array of mouse tissues. Biotechniques 45, 613–614 (2008).
27. L. K. Johnston, C. R. Rims, S. E. Gill, J. K. McGuire, A. M. Manicone, Pulmonary macrophage subpopulations in the induction and resolution of acute lung injury. Am. J. Respir. Cell Mol. Biol. 47, 417–426 (2012).
28. A. Sica, A. Mantovani, Macrophage plasticity and polarization: In vivo veritas. J. Clin. Investig. 122, 787–795 (2012).
29. P. A. Ward, G. W. Hunninghake, Lung inflammation and fibrosis. Am. J. Respir. Critical Care Med. 157, S123–S129 (1998).
30. A. H. Gifford, M. Matsuoka, L. Y. Ghoda, R. J. Homer, R. I. Enelow, Chronic inflammation and lung fibrosis: Pleotropic syndromes but limited distinct phenotypes. Mucosal Immunol. 5, 480–484 (2012).
31. K. Shenderov, S. L. Collins, J. D. Powell, M. R. Horton, Immune dysregulation as a driver of idiopathic pulmonary fibrosis. J. Clin. Investig. 131, e143226 (2021).
32. N. Khalil, O. Bereznay, M. Sporn, A. H. Greenberg, Macrophage production of transforming growth factor beta and fibroblast collagen synthesis in chronic pulmonary inflammation. J. Exp. Med. 170, 727–737 (1989).
33. T. A. Wynn, K. M. Vannella, Macrophages in tissue repair, regeneration, and fibrosis. Immunity 44, 450–462 (2016).
34. M. Sospedra, R. Martin, Immunology of multiple sclerosis. Semin. Neurol. 36, 115–127 (2016).
35. A. V. Garg, N. Amatya, K. Chen, J. A. Cruz, P. Grover, N. Whibley, H. R. Conti, G. H. Mir, T. Sirakova, E. C. Childs, T. E. Smithgall, P. S. Biswas, J. K. Kolls, M. J. McGeachy, P. E. Kolattukudy, S. L. Gaffen, MCPIP1 endoribonuclease activity negatively regulates interleukin-17-mediated signaling and inflammation. Immunity 43, 475–487 (2015).
36. A. Ben-Nun, H. Wekerle, I. R. Cohen, The rapid isolation of clonable antigen-specific T lymphocyte lines capable of mediating autoimmune encephalomyelitis. Eur. J. Immunol. 11, 195–199 (1981).
37. D. G. Ando, J. Clayton, D. Kono, J. L. Urban, E. E. Sercarz, Encephalitogenic T cells in the B10.PL model of experimental allergic encephalomyelitis (EAE) are of the Th-1 lymphokine subtype. Cell. Immunol. 124, 132–143 (1989).
38. C. L. Langrish, Y. Chen, W. M. Blumenschein, J. Mattson, B. Basham, J. D. Sedgwick, T. McClanahan, R. A. Kastelein, D. J. Cua, IL-23 drives a pathogenic T cell population that induces autoimmune inflammation. J. Exp. Med. 201, 233–240 (2005).
39. M. A. Kroenke, T. J. Carlson, A. V. Andjelkovic, B. M. Segal, IL-12- and IL-23-modulated T cells induce distinct types of EAE based on histology, CNS chemokine profile, and response to cytokine inhibition. J. Exp. Med. 205, 1535–1541 (2008).
40. L. Monin, J. E. Gudjonsson, E. E. Childs, N. Amatya, X. Xing, A. H. Verma, B. M. Coleman, A. V. Garg, M. Killeen, A. Mathers, N. L. Ward, S. L. Gaffen, MCPIP1/Regnase-1 restricts IL-17A- and IL-17C-dependent skin inflammation. J. Immunol. 198, 767–775 (2017).
41. T. Yamazaki, X. O. Yang, Y. Chung, A. Fukunaga, R. Nurieva, B. Pappu, N. Martin-Orozco, H. S. Kang, L. Ma, A. D. Panopoulos, S. Craig, S. S. Watowich, A. M. Jetten, Q. Tian, C. Dong, CCR6 regulates the migration of inflammatory and regulatory T cells. J. Immunol. 181, 8391–8401 (2008).
42. M. Ito, K. Komai, S. Mise-Omata, M. Iizuka-Koga, Y. Noguchi, T. Kondo, R. Sakai, K. Matsuo, T. Nakayama, O. Yoshie, H. Nakatsukasa, S. Chikuma, T. Shichita, A. Yoshimura, Brain regulatory T cells suppress astrogliosis and potentiate neurological recovery. Nature 565, 246–250 (2019).
43. M. J. C. Jordão, R. Sankowski, S. M. Brendecke, S. G. Locatelli, Y. H. Tai, T. L. Tay, E. Schramm, S. Armbruster, N. Hagemeyer, O. Groß, D. Mai, Ö. Çiçek, T. Falk, M. Kerschensteiner, D. Grün, M. Prinz, Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation. Science 363, eaat7554 (2019).
44. S. E. Hickman, N. D. Kingery, T. K. Ohsumi, M. L. Borowsky, L. C. Wang, T. K. Means, J. El Khoury, The microglial sensome revealed by direct RNA sequencing. Nature Neurosci. 16, 1896–1905 (2013).
45. C. Ryckman, K. Vandal, P. Rouleau, M. Talbot, P. A. Tessier, Proinflammatory activities of S100: Proteins S100A8, S100A9, and S100A8/A9 induce neutrophil chemotaxis and adhesion. J. Immunol. 170, 3233–3242 (2003).
46. T. E. Sutherland, N. Logan, D. Rückerl, A. A. Humbles, S. M. Allan, V. Papayannopoulos, B. Stockinger, R. M. Maizels, J. E. Allen, Chitinase-like proteins promote IL-17-mediated neutrophilia in a tradeoff between nematode killing and host damage. Nature Immunol. 15, 1116–1125 (2014).
47. T. Carlson, M. Kroenke, P. Rao, T. E. Lane, B. Segal, The Th17-ELR+ CXC chemokine pathway is essential for the development of central nervous system autoimmune disease. J. Exp. Med. 205, 811–823 (2008).
48. J. M. Rumble, A. K. Huber, G. Krishnamoorthy, A. Srinivasan, D. A. Giles, X. Zhang, L. Wang, B. M. Segal, Neutrophil-related factors as biomarkers in EAE and MS. J. Exp. Med. 212, 23–35 (2015).
49. K. Kennedy, R. Strieter, S. Kunkel, N. Lukacs, W. Karpus, Acute and relapsing experimental autoimmune encephalomyelitis are regulated by differential expression of the CC chemokines macrophage inflammatory protein-1alpha and monocyte chemotactic protein-1. J. Meuroimmunol. 92, 98–108 (1998).
50. S. Youssef, G. Wildbaum, N. Karin, Prevention of experimental autoimmune encephalomyelitis by MIP-1alpha and MCP-1 naked DNA vaccines. J. Autoimmun. 13, 21–29 (1999).
51. M. Soleimani, A. Soleymani, N. Seyyedirad, Elevated CSF concentration of CCL3 and CCL4 in relapsing remitting multiple sclerosis patients. J. Immunoassay Immunochem. 40, 378–385 (2019).
52. R. A. Rudick, J. C. Lee, J. Simon, E. Fisher, Significance of T2 lesions in multiple sclerosis: A 13-year longitudinal study. Ann. Neurol. 60, 236–242 (2006).
53. J. P. Mostert, M. W. Koch, C. Steen, D.J. Heersema, J. C. DeGroot, J. De Keyser, T2 lesions and rate of progression of disability in multiple sclerosis. Eur. J. Neurol. 17, 1471–1475 (2010).
54. D. C. Rockey, P. D. Bell, J. A. Hill, Fibrosis--A common pathway to organ injury and failure. N. Engl. J. Med. 372, 1138–1149 (2015).
55. G. Bagnato, S. Harari, Cellular interactions in the pathogenesis of interstitial lung diseases. Eur. Respir. Rev. 24, 102–114 (2015).
56. B. Aubé, S. A. Lévesque, A. Paré, É. Chamma, H. Kébir, R. Gorina, M. A. Lécuyer, J. I. Alvarez, Y. De Koninck, B. Engelhardt, A. Prat, D. Côté, S. Lacroix, Neutrophils mediate blood-spinal cord barrier disruption in demyelinating neuroinflammatory diseases. J. Immunol. 193, 2438–2454 (2014).
57. E. R. Pierson, C. A. Wagner, J. M. Goverman, The contribution of neutrophils to CNS autoimmunity. Clin. Immunol. 189, 23–28 (2018).
58. J. R. Bradley, TNF-mediated inflammatory disease. J. Pathol. 214, 149–160 (2008).
59. T. Tanaka, T. Kishimoto, Targeting interleukin-6: All the way to treat autoimmune and inflammatory diseases. Int. J. Biol. Sci. 8, 1227–1236 (2012).
60. M. Yoshinaga, Y. Nakatsuka, A. Vandenbon, D. Ori, T. Uehata, T. Tsujimura, Y. Suzuki, T. Mino, O. Takeuchi, Regnase-1 maintains iron homeostasis via the degradation of transferrin receptor 1 and prolyl-hydroxylase-domain-containing protein 3 mRNAs. Cell Rep. 19, 1614–1630 (2017).
61. S. Omiya, Y. Omori, M. Taneike, T. Murakawa, J. Ito, Y. Tanada, K. Nishida, O. Yamaguchi, T. Satoh, A. M. Shah, S. Akira, K. Otsu, Cytokine mRNA degradation in cardiomyocytes restrains sterile inflammation in pressure-overloaded hearts. Circulation 141, 667–677 (2020).
62. K. N. Gibson-Corley, A. W. Boyden, M. R. Leidinger, A. M. Lambertz, G. Ofori-Amanfo, P. W. Naumann, J. A. Goeken, N. J. Karandikar, A method for histopathological study of the multifocal nature ofspinal cord lesions in murine experimental autoimmune encephalomyelitis. PeerJ 4, e1600 (2016).
63. A. J. Thompson, B. L. Banwell, F. Barkhof, W. M. Carroll, T. Coetzee, G. Comi, J. Correale, F. Fazekas, M. Filippi, M. S. Freedman, K. Fujihara, S. L. Galetta, H. P. Hartung, L. Kappos, F. D. Lublin, R. A. Marrie, A. E. Miller, D. H. Miller, X. Montalban, E. M. Mowry, P. S. Sorensen, M. Tintoré, A. L. Traboulsee, M. Trojano, B. M. J. Uitdehaag, S. Vukusic, E. Waubant, B. G. Weinshenker, S. C. Reingold, J. A. Cohen, Diagnosis of multiple sclerosis: 2017 revisions of the McDonald criteria. Lancet Neurol. 17, 162–173 (2018).
64. H. Lian, E. Roy, H. Zheng, Protocol for primary microglial culture preparation. Bio-protocol 6, e1989 (2016).
65. G. Matute-Bello, G. Downey, B. B. Moore, S. D. Groshong, M. A. Matthay, A. S. Slutsky, W. M. Kuebler, An official american thoracic society workshop report: Features and measurements of experimental acute lung injury in animals. Am. J. Respir. Cell Mol. Biol. 44, 725–738 (2011).
66. T. P. Sheahan, A. C. Sims, S. R. Leist, A. Schäfer, J. Won, A. J. Brown, S. A. Montgomery, A. Hogg, D. Babusis, M. O. Clarke, J. E. Spahn, L. Bauer, S. Sellers, D. Porter, J. Y. Feng, T. Cihlar, R. Jordan, M. R. Denison, R. S. Baric, Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV. Nat. Commun. 11, 222 (2020).
67. T. Ashcroft, J. M. Simpson, V. Timbrell, Simple method of estimating severity of pulmonary fibrosis on a numerical scale. J. Clin. Pathol. 41, 467–470 (1988).
68. Y. Hao, S. Hao, E. Andersen-Nissen, W. M. Mauck, S. Zheng, A. Butler, M. J. Lee, A. J. Wilk, C. Darby, M. Zager, P. Hoffman, M. Stoeckius, E. Papalexi, E. P. Mimitou, J. Jain, A. Srivastava, T. Stuart, L. M. Fleming, B. Yeung, A. J. Rogers, J. M. McElrath, C. A. Blish, R. Gottardo, P. Smibert, R. Satija, Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
69. I. Korsunsky, N. Millard, J. Fan, K. Slowikowski, F. Zhang, K. Wei, Y. Baglaenko, M. Brenner, P. R. Loh, S. Raychaudhuri, Fast, sensitive and accurate integration ofsingle-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
70. H. Wickham, D. Navarro, T. L. Pedersen, ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, ed. 2, 2016).
71. D. Kim, B. Langmead, S. L. Salzberg, HISAT: A fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
72. E. Afgan, D. Baker, B. Batut, M. van den Beek, D. Bouvier, M. Cech, J. Chilton, D. Clements, N. Coraor, B. A. Grüning, A. Guerler, J. Hillman-Jackson, S. Hiltemann, V. Jalili, H. Rasche, N. Soranzo, J. Goecks, J. Taylor, A. Nekrutenko, D. Blankenberg, The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46, W537–W544 (2018).
73. P. D. Thomas, M. J. Campbell, A. Kejariwal, H. Mi, B. Karlak, R. Daverman, K. Diemer, A. Muruganujan, A. Narechania, PANTHER: A library of protein families and subfamilies indexed by function. Genome Res. 13, 2129–2141 (2003).