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The m6A methyltransferase METTL3 drives neuroinflammation and neurotoxicity through stabilizing BATF mRNA in microglia

Cell Death & Differentiation volume 32, pages 100–117 (2025)Cite this article

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Abstract

Persistent neuroinflammation and progressive neuronal loss are defining features of acute brain injury including traumatic brain injury (TBI) and cerebral stroke. Microglia, the most abundant type of brain-resident immune cells, continuously surveil the environment and play a central role in shaping the inflammatory state of the central nervous system (CNS). In the study, we discovered that the protein expression of METTL3 (a m6A methyltransferase) was upregulated in inflammatory microglia independent of increased Mettl3 gene transcription following TBI in both human and mouse subjects. Subsequently, we identified TRIP12, a HECT-___domain E3 ubiquitin ligase, as a negative regulator of METTL3 protein expression by facilitating METTL3 K48-linked polyubiquitination. Importantly, selective ablation of Mettl3 inhibited microglial pathogenic activities, diminished neutrophil infiltration, rescued neuronal loss and facilitated functional recovery post-TBI. Using MeRIP-seq and CUT&Tag sequencing, we identified that METTL3 promoted the expression of Basic Leucine Zipper Transcriptional Factor ATF-Like (BATF), which in turn directly bound to a cohort of characteristic inflammatory cytokines and chemokine genes. Enhanced activities of BATF in microglia elicited TNF-dependent neurotoxicity and can also promote neutrophil recruitment through releasing CXCL2. Pharmacological inhibition of METTL3 using a BBB-penetrating drug-loaded nano-system showed satisfactory therapeutic effects in both TBI and stroke mouse models. Collectively, our findings identified METTL3-m6A-BATF axis as a potential therapeutic target for terminating detrimental neuroinflammation and progressive neuronal loss following acute brain injury.

METTL3 protein is significantly up-regulated in inflammatory microglia due to the decreased proteasomal degradation mediated by TRIP12 and ERK-USP5 pathways. METTL3 stabilized BATF mRNA stability and promoted BATF expression through the m6A-IGF2BP2-dependent mechanism. Elevated expression of BATF elicits a pro-inflammatory gene program in microglia, and aggravates neuroinflammatory response including local immune responses and peripheral immune cell infiltration. Genetic deletion or pharmaceutically targeting METTL3-BATF axis suppressed microglial pro-inflammatory activities and promoted neurological recovery following TBI and stroke.

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Fig. 1: Decreased proteasomal degradation of METTL3 protein and enhanced m6A modifications in inflammatory microglia following TBI.
Fig. 2: Microglial METTL3 knockout alleviated TBI-induced neuroinflammatory response.
Fig. 3: Conditional knockout of METTL3 in microglia preserved neuronal integrity and promoted neurological recovery after TBI.
Fig. 4: METTL3 promoted the expression of BATF in an m6A-IGF2BP2 dependent way.
Fig. 5: BATF drives a pro-inflammatory transcriptional profile in microglia.
Fig. 6: METTL3-m6A-BATF axis involved in microglia pathogenic activities and brain injury after cerebral ischemic stroke.
Fig. 7: Engineered nanoparticles mediated delivery of METTL3 inhibitor alleviate neuroinflammation and promote neurological recovery after TBI.

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Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request.

References

  1. Prinz M, Masuda T, Wheeler MA, Quintana FJ. Microglia and central nervous system-associated macrophages-from origin to disease modulation. Annu Rev Immunol. 2021;39:251–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Crapser JD, Arreola MA, Tsourmas KI, Green KN. Microglia as hackers of the matrix: sculpting synapses and the extracellular space. Cell Mol Immunol. 2021;18:2472–88.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Vecchiarelli HA, Tremblay M. Microglial transcriptional signatures in the central nervous system: toward a future of unraveling their function in health and disease. Annu Rev Genet. 2023;57:65–86.

    Article  CAS  PubMed  Google Scholar 

  4. Silvin A, Qian J, Ginhoux F. Brain macrophage development, diversity and dysregulation in health and disease. Cell Mol Immunol. 2023;20:1277–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Borst K, Dumas AA, Prinz M. Microglia: Immune and non-immune functions. Immunity. 2021;54:2194–208.

    Article  CAS  PubMed  Google Scholar 

  6. Keane L, Antignano I, Riechers SP, Zollinger R, Dumas AA, Offermann N, et al. mTOR-dependent translation amplifies microglia priming in aging mice. J Clin Investig. 2021;131:e132727.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Prinz M, Jung S, Priller J. Microglia biology: one century of evolving concepts. Cell. 2019;179:292–311.

    Article  CAS  PubMed  Google Scholar 

  8. Castro-Sánchez S, García-Yagüe ÁJ, Kügler S, Lastres-Becker I. CX3CR1-deficient microglia shows impaired signalling of the transcription factor NRF2: Implications in tauopathies. Redox Biol. 2019;22:101118.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Islam A, Choudhury ME, Kigami Y, Utsunomiya R, Matsumoto S, Watanabe H, et al. Sustained anti-inflammatory effects of TGF-β1 on microglia/macrophages. Biochim Biophys Acta Mol Basis Dis. 2018;1864:721–34.

    Article  CAS  PubMed  Google Scholar 

  10. Shi K, Zhang J, Dong JF, Shi FD. Dissemination of brain inflammation in traumatic brain injury. Cell Mol Immunol. 2019;16:523–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Willis EF, MacDonald KPA, Nguyen QH, Garrido AL, Gillespie ER, Harley SBR, et al. Repopulating microglia promote brain repair in an IL-6-dependent manner. Cell. 2020;180:833–46.e16.

    Article  CAS  PubMed  Google Scholar 

  12. Chen S, Dong Z, Cheng M, Zhao Y, Wang M, Sai N, et al. Homocysteine exaggerates microglia activation and neuroinflammation through microglia localized STAT3 overactivation following ischemic stroke. J Neuroinflamm. 2017;14:187.

    Article  CAS  Google Scholar 

  13. Greenhalgh AD, David S, Bennett FC. Immune cell regulation of glia during CNS injury and disease. Nat Rev Neurosci. 2020;21:139–52.

    Article  CAS  PubMed  Google Scholar 

  14. Jin X, Yamashita T. Microglia in central nervous system repair after injury. J Biochem. 2016;159:491–6.

    Article  CAS  PubMed  Google Scholar 

  15. Lan X, Han X, Li Q, Yang QW, Wang J. Modulators of microglial activation and polarization after intracerebral haemorrhage. Nat Rev Neurol. 2017;13:420–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Holtman IR, Skola D, Glass CK. Transcriptional control of microglia phenotypes in health and disease. J Clin Investig. 2017;127:3220–9.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Wu Z, Shi Y, Lu M, Song M, Yu Z, Wang J, et al. METTL3 counteracts premature aging via m6A-dependent stabilization of MIS12 mRNA. Nucleic Acids Res. 2020;48:11083–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Zhou C, Molinie B, Daneshvar K, Pondick JV, Wang J, Van Wittenberghe N, et al. Genome-wide maps of m6A circRNAs identify widespread and cell-type-specific methylation patterns that are distinct from mRNAs. Cell Rep. 2017;20:2262–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mathiyalagan P, Adamiak M, Mayourian J, Sassi Y, Liang Y, Agarwal N, et al. FTO-dependent N(6)-methyladenosine regulates cardiac function during remodeling and repair. Circulation. 2019;139:518–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Dorn LE, Lasman L, Chen J, Xu X, Hund TJ, Medvedovic M, et al. The N(6)-methyladenosine mRNA methylase METTL3 controls cardiac homeostasis and hypertrophy. Circulation. 2019;139:533–45.

    Article  CAS  PubMed  Google Scholar 

  21. Shi H, Wei J, He C. Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Mol Cell. 2019;74:640–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Liu T, Wei Q, Jin J, Luo Q, Liu Y, Yang Y, et al. The m6A reader YTHDF1 promotes ovarian cancer progression via augmenting EIF3C translation. Nucleic Acids Res. 2020;48:3816–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Wang JN, Wang F, Ke J, Li Z, Xu CH, Yang Q, et al. Inhibition of METTL3 attenuates renal injury and inflammation by alleviating TAB3 m6A modifications via IGF2BP2-dependent mechanisms. Sci Transl Med. 2022;14:eabk2709.

    Article  CAS  PubMed  Google Scholar 

  24. Ma S, Sun B, Duan S, Han J, Barr T, Zhang J, et al. YTHDF2 orchestrates tumor-associated macrophage reprogramming and controls antitumor immunity through CD8(+) T cells. Nat Immunol. 2023;24:255–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Weng H, Huang F, Yu Z, Chen Z, Prince E, Kang Y, et al. The m(6)A reader IGF2BP2 regulates glutamine metabolism and represents a therapeutic target in acute myeloid leukemia. Cancer Cell. 2022;40:1566–82.e10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Zhang X, Yin H, Zhang X, Jiang X, Liu Y, Zhang H, et al. N6-methyladenosine modification governs liver glycogenesis by stabilizing the glycogen synthase 2 mRNA. Nat Commun. 2022;13:7038.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Pham D, Silberger DJ, Nguyen KN, Gao M, Weaver CT, Hatton RD. Batf stabilizes Th17 cell development via impaired Stat5 recruitment of Ets1-Runx1 complexes. Embo J. 2023;42:e109803.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Zhang X, Zhang C, Qiao M, Cheng C, Tang N, Lu S, et al. Depletion of BATF in CAR-T cells enhances antitumor activity by inducing resistance against exhaustion and formation of central memory cells. Cancer Cell. 2022;40:1407–22.e7.

    Article  CAS  PubMed  Google Scholar 

  29. Huang TY, Hirota M, Sasaki D, Kalra RS, Chien HC, Tamai M, et al. Phosphoenolpyruvate regulates the Th17 transcriptional program and inhibits autoimmunity. Cell Rep. 2023;42:112205.

    Article  CAS  PubMed  Google Scholar 

  30. Wu X, Khatun A, Kasmani MY, Chen Y, Zheng S, Atkinson S, et al. Group 3 innate lymphoid cells require BATF to regulate gut homeostasis in mice. J Exp Med. 2022;219:e20211861.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Bae S, Kim K, Kang K, Kim H, Lee M, Oh B, et al. RANKL-responsive epigenetic mechanism reprograms macrophages into bone-resorbing osteoclasts. Cell Mol Immunol. 2023;20:94–109.

    Article  CAS  PubMed  Google Scholar 

  32. Choi JK, Yu CR, Bing SJ, Jittayasothorn Y, Mattapallil MJ, Kang M, et al. IL-27-producing B-1a cells suppress neuroinflammation and CNS autoimmune diseases. Proc Natl Acad Sci USA. 2021;118:e2109548118.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Gosselin D, Skola D, Coufal NG, Holtman IR, Schlachetzki JCM, Sajti E, et al. An environment-dependent transcriptional network specifies human microglia identity. Science. 2017;356:eaal3222.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Zheng P, Zhang N, Ren D, Yu C, Zhao B, Zhang Y. Integrated spatial transcriptome and metabolism study reveals metabolic heterogeneity in human injured brain. Cell Rep. Med. 2023;4:101057.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Yang Z, Lin P, Chen B, Zhang X, Xiao W, Wu S, et al. Autophagy alleviates hypoxia-induced blood-brain barrier injury via regulation of CLDN5 (claudin 5). Autophagy. 2021;17:3048–67.

    Article  CAS  PubMed  Google Scholar 

  36. Luo J, Wu X, Liu H, Cui W, Guo W, Guo K, et al. Antagonism of protease-activated receptor 4 protects against traumatic brain injury by suppressing neuroinflammation via inhibition of Tab2/NF-κB signaling. Neurosci Bull. 2021;37:242–54.

    Article  CAS  PubMed  Google Scholar 

  37. Yang L, Han B, Zhang Z, Wang S, Bai Y, Zhang Y, et al. Extracellular vesicle-mediated delivery of circular RNA SCMH1 promotes functional recovery in rodent and nonhuman primate ischemic stroke models. Circulation. 2020;142:556–74.

    Article  CAS  PubMed  Google Scholar 

  38. Gao XQ, Zhang YH, Liu F, Ponnusamy M, Zhao XM, Zhou LY, et al. The piRNA CHAPIR regulates cardiac hypertrophy by controlling METTL3-dependent N(6)-methyladenosine methylation of Parp10 mRNA. Nat Cell Biol. 2020;22:1319–31.

    Article  CAS  PubMed  Google Scholar 

  39. Zhang S, Wu X, Wang J, Shi Y, Hu Q, Cui W, et al. Adiponectin/AdiopR1 signaling prevents mitochondrial dysfunction and oxidative injury after traumatic brain injury in a SIRT3 dependent manner. Redox Biol. 2022;54:102390.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Sun HL, Zhu AC, Gao Y, Terajima H, Fei Q, Liu S, et al. Stabilization of ERK-phosphorylated METTL3 by USP5 increases m(6)A methylation. Mol Cell. 2020;80:633–47.e7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Shin MK, Vázquez-Rosa E, Koh Y, Dhar M, Chaubey K, Cintrón-Pérez CJ, et al. Reducing acetylated tau is neuroprotective in brain injury. Cell. 2021;184:2715–32.e23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Luo S, Liao C, Zhang L, Ling C, Zhang X, Xie P, et al. METTL3-mediated m6A mRNA methylation regulates neutrophil activation through targeting TLR4 signaling. Cell Rep. 2023;42:112259.

    Article  CAS  PubMed  Google Scholar 

  43. Chen Y, Zander RA, Wu X, Schauder DM, Kasmani MY, Shen J, et al. BATF regulates progenitor to cytolytic effector CD8(+) T cell transition during chronic viral infection. Nat Immunol. 2021;22:996–1007.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Seo H, González-Avalos E, Zhang W, Ramchandani P, Yang C, Lio CJ, et al. BATF and IRF4 cooperate to counter exhaustion in tumor-infiltrating CAR T cells. Nat Immunol. 2021;22:983–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Pham D, Moseley CE, Gao M, Savic D, Winstead CJ, Sun M, et al. Batf pioneers the reorganization of chromatin in developing effector T cells via Ets1-dependent recruitment of Ctcf. Cell Rep. 2019;29:1203–20.e7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Jiang S, Willox B, Zhou H, Holthaus AM, Wang A, Shi TT, et al. Epstein-Barr virus nuclear antigen 3C binds to BATF/IRF4 or SPI1/IRF4 composite sites and recruits Sin3A to repress CDKN2A. Proc Natl Acad Sci USA. 2014;111:421–6.

    Article  CAS  PubMed  Google Scholar 

  47. Ndoja A, Reja R, Lee SH, Webster JD, Ngu H, Rose CM, et al. Ubiquitin ligase COP1 suppresses neuroinflammation by degrading c/EBPβ in microglia. Cell. 2020;182:1156–69.e12.

    Article  CAS  PubMed  Google Scholar 

  48. Wu X, Kasmani MY, Zheng S, Khatun A, Chen Y, Winkler W, et al. BATF promotes group 2 innate lymphoid cell-mediated lung tissue protection during acute respiratory virus infection. Sci Immunol. 2022;7:eabc9934.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Wang T, Zhou Y, Zhou Z, Zhang P, Yan R, Sun L, et al. Secreted protease PRSS35 suppresses hepatocellular carcinoma by disabling CXCL2-mediated neutrophil extracellular traps. Nat Commun. 2023;14:1513.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. McDowell SAC, Milette S, Doré S, Yu MW, Sorin M, Wilson L, et al. Obesity alters monocyte developmental trajectories to enhance metastasis. J Exp Med. 2023;220:e20220509.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Yankova E, Blackaby W, Albertella M, Rak J, De Braekeleer E, Tsagkogeorga G, et al. Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature. 2021;593:597–601.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Kim DG, Bynoe MS. A2A adenosine receptor modulates drug efflux transporter P-glycoprotein at the blood-brain barrier. J Clin Investig. 2016;126:1717–33.

    Article  PubMed  PubMed Central  Google Scholar 

  53. Zhang C, Jiang M, Wang WQ, Zhao SJ, Yin YX, Mi QJ, et al. Selective mGluR1 negative allosteric modulator reduces blood-brain barrier permeability and cerebral edema after experimental subarachnoid hemorrhage. Transl Stroke Res. 2020;11:799–811.

    Article  CAS  PubMed  Google Scholar 

  54. Han B, Jiang W, Cui P, Zheng K, Dang C, Wang J, et al. Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation. Genome Med. 2021;13:47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Funding

This work was supported by the State Key Program of the National Natural Science Foundation of China (Nos. 81630027 and 82130038, to YQ). And the authors would like to thank to Clinical Research Center for Neurosurgical Diseases of Shaanxi Province and Shaanxi International Science & Technology Cooperation Base for their support.

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  1. These authors contributed equally: Xun Wu, Haixiao Liu, Jin Wang.

Authors and Affiliations

  1. Department of Neurosurgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, 710032, Shaanxi, China

    Xun Wu, Haixiao Liu, Shenghao Zhang, Qing Hu, Tinghao Wang, Wenxing Cui, Yingwu Shi, Hao Bai, Jinpeng Zhou, Liying Han, Leiyang Li, Tianzhi Zhao, Dayun Feng, Wei Guo, Shunnan Ge & Yan Qu

  2. Department of Neurosurgery, Zhejiang Provincial People’s Hospital, Hangzhou, 310000, Zhejiang, China

    Jin Wang

  3. Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China

    Yang Wu

  4. Department of Neurosurgery, West Theater General Hospital, Chengdu, 610083, Sichuan, China

    Jianing Luo

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  1. Xun Wu
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Contributions

YQ, SG and WG designed the study. XW, HL, SZ, and WC performed animal studies. JW, QH and YS performed the in vitro experiments. HB and LL were responsible for human clinical studies. The images were photographed by YW and TZ. JL, PZ, DF, and LH helped to analyze MeRIP-seq, RNA-seq and CUT&Tag data. XW, HL, and JW wrote the manuscript. SG revised the manuscript.

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Correspondence to Wei Guo, Shunnan Ge or Yan Qu.

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The authors declare no competing interests.

Ethics

All animal experimental procedures were approved by the Ethics Committee of the Fourth Military Medical University (IACUC- 20210556) and performed according to the Animal Research: Reporting in Vivo Experiments (ARRIVE) guidelines. All procedures involving the participants were granted ethical approval by the Ethics Committee of Tangdu Hospital, Fourth Military Medical University (TD-202103–006). Furthermore, the human research conducted in this study adhered to the principles outlined in the Helsinki Declaration, and written informed consent was obtained from each patient or their legal surrogate.

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Wu, X., Liu, H., Wang, J. et al. The m6A methyltransferase METTL3 drives neuroinflammation and neurotoxicity through stabilizing BATF mRNA in microglia. Cell Death Differ 32, 100–117 (2025). https://doi.org/10.1038/s41418-024-01329-y

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