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

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.

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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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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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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 (2024). https://doi.org/10.1038/s41418-024-01329-y

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