TET3 is a common epigenetic immunomodulator of pathogenic macrophages
Beibei Liu, Yangyang Dai, Zixin Wang, Jiahui Song, Yushu Du, Haining Lv, Stefania Bellone, Yang-Hartwich Yang, Andrew Kennedy, Songying Zhang, Muthukumaran Venkatachalapathy, Yulia Surovtseva, Penghua Wang, Gordon G. Carmichael, Hugh S. Taylor, Xuchen Zhang, Da Li, Yingqun Huang
Beibei Liu, Yangyang Dai, Zixin Wang, Jiahui Song, Yushu Du, Haining Lv, Stefania Bellone, Yang-Hartwich Yang, Andrew Kennedy, Songying Zhang, Muthukumaran Venkatachalapathy, Yulia Surovtseva, Penghua Wang, Gordon G. Carmichael, Hugh S. Taylor, Xuchen Zhang, Da Li, Yingqun Huang
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Research Article Hepatology Immunology Inflammation

TET3 is a common epigenetic immunomodulator of pathogenic macrophages

Abstract

Through a combination of single-cell/single-nucleus RNA-Seq (sc/snRNA-Seq) data analysis, immunohistochemistry, and primary macrophage studies, we have identified pathogenic macrophages characterized by Tet methylcytosine dioxygenase 3 (TET3) overexpression (Toe-Macs) in 3 major human diseases associated with chronic inflammation: metabolic dysfunction–associated steatohepatitis (MASH), non–small cell lung cancer (NSCLC), and endometriosis. These macrophages are induced by common factors present in the disease microenvironment (DME). Crucially, the universal reliance on TET3 overexpression among these macrophages enabled their selective elimination as a single population, irrespective of heterogeneity in other molecular markers. In mice, depleting these macrophages via myeloid-specific Tet3 KO markedly mitigated disease progression, and the therapeutic effects were recapitulated pharmacologically using a TET3-specific small-molecule degrader. Through an unexpected mode of action, TET3 epigenetically regulated the expression of multiple genes key to the generation and maintenance of an inflammatory/immunosuppressive DME. We propose that Toe-Macs are a unifying feature of pathogenic macrophages that could be therapeutically targeted to treat MASH, NSCLC, endometriosis, and potentially other chronic inflammatory diseases.

Authors

Beibei Liu, Yangyang Dai, Zixin Wang, Jiahui Song, Yushu Du, Haining Lv, Stefania Bellone, Yang-Hartwich Yang, Andrew Kennedy, Songying Zhang, Muthukumaran Venkatachalapathy, Yulia Surovtseva, Penghua Wang, Gordon G. Carmichael, Hugh S. Taylor, Xuchen Zhang, Da Li, Yingqun Huang

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Figure 3

TET3 epigenetically regulates TGFB1, NLRP3, IL1B, and CCL2 expression through interaction with phosphorylated STAT3.

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TET3 epigenetically regulates TGFB1, NLRP3, IL1B, and CCL2 expression th...
(A) Schematic of the human TGFB1 promoter. Numbers depict nucleotide positions relative to the transcription start site labeled +1. The PCR-amplified region is marked in red, with the zoomed-in sequence shown underneath. The PCR primer sequences are underlined. (B) MDMs were infected with Ad-GFP or Ad-TET3 for 16 hours. Chromatins were prepared for ChIP-qPCR analysis to detect enrichment of the specific TGFB1 promoter region outlined in A. (C) MDMs were infected with Ad-GFP (lane 2) or Ad-TET3 (lane 3) for 24 hours, followed by co-IP using anti-Flag antibody. Western blot analysis was carried out using anti-TET3 or anti-STAT3 (Y705) antibodies. Lane 1 shows 5% of input from Ad-TET3–infected cells. IB, immunoblot. (D and E) MDMs were treated as in B. Genomic DNA was collected and subjected to hMeDIP-qPCR (D) and MeDIP-qPCR (E). (F) Schematic of the human NLRP3 promoter. (G) MDMs were treated as in B, followed by ChIP-qPCR. (H) MDMs were treated as in B, followed by hMeDIP-qPCR. (I) Schematic of the human IL1B promoter. The STAT3-binding site is highlighted blue. (J) MDMs were treated as in B, followed by ChIP-qPCR. (K) MDMs were treated as in B, followed by hMeDIP-qPCR. (L) Basal IL1B expression in MDMs infected with Ad-GFP or Ad-TET3 was assessed by qRT-PCR. (M) Schematic of the human CCL2 promoter. The STAT3-binding site is highlighted blue. (N) MDMs were treated as in B, followed by ChIP-qPCR. In B, G, J, and N, 5 × 105 cells per ChIP were used. All data represent the mean ± SEM. *P < 0.05, **P < 0.01, and ***P < 0.001, by 2-tailed Student’s t test. Western blot data are representative of 2 biological repeats. chr, chromosome.