Targeting N-acetyltransferase 10 reprograms Treg function to enhance anti–PD-1 immunotherapy sensitivity in murine lung tumors
Xuewei Qi, Dan Cui, Xiao Li, Wenfan Fu, Handong Ma, Wenting Guo, Jiabao Wang, Jiaxi Song, Jiaxin Ma, Jing Yang, Haoyu Yu, Yuting Hong, Qian Wang, Susu Luo, Jia Wang, Baixing Wu, Shanshan Li, Hao Cheng, Min Cheng, Bin Li, Kaiming Zhang, Jia Li, Fengyin Li
Xuewei Qi, Dan Cui, Xiao Li, Wenfan Fu, Handong Ma, Wenting Guo, Jiabao Wang, Jiaxi Song, Jiaxin Ma, Jing Yang, Haoyu Yu, Yuting Hong, Qian Wang, Susu Luo, Jia Wang, Baixing Wu, Shanshan Li, Hao Cheng, Min Cheng, Bin Li, Kaiming Zhang, Jia Li, Fengyin Li
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Research Article Cell biology Oncology

Targeting N-acetyltransferase 10 reprograms Treg function to enhance anti–PD-1 immunotherapy sensitivity in murine lung tumors

Abstract

A significant challenge for improving the efficacy of immune checkpoint blockade (ICB) therapy is the concurrent activation of Tregs, which can dampen antitumor responses. Thus, elucidating the mechanisms that maintain Treg-suppressive function within the tumor microenvironment is critical. Here, we identified an accumulation of N-acetyltransferase 10–modified (NAT10-modified) RNA, particularly in NAT10+FOXP3+ Tregs, in human non–small cell lung cancer. Genetic ablation of Nat10 in tumor-infiltrating (TI) Tregs, or pharmacological inhibition of NAT10 expression, significantly reduced the PD-1+ Treg/CD8+ T cell ratio. These effects were accompanied by an increase in IFN-γ+ Tregs, a reduction in the immunosuppressive activity of Tregs, and inhibition of tumor progression. Mechanistically, NAT10 promotes TI Treg infiltration and activation independently of its RNA-modifying function by directly interacting with FOXP3 and chromatin, modulating local 3D chromatin contacts. Combined administration of anti–PD-1 antibodies and a NAT10 inhibitor further impaired TI Treg–mediated immunosuppression, leading to enhanced tumor control. Our findings demonstrate that NAT10 is a key regulator of TI Treg fragility and function and that its inhibition may enhance the therapeutic efficacy of ICB.

Authors

Xuewei Qi, Dan Cui, Xiao Li, Wenfan Fu, Handong Ma, Wenting Guo, Jiabao Wang, Jiaxi Song, Jiaxin Ma, Jing Yang, Haoyu Yu, Yuting Hong, Qian Wang, Susu Luo, Jia Wang, Baixing Wu, Shanshan Li, Hao Cheng, Min Cheng, Bin Li, Kaiming Zhang, Jia Li, Fengyin Li

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Figure 5

NAT10 interacts with FOXP3 to facilitate the Treg superenhancer establishment.

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NAT10 interacts with FOXP3 to facilitate the Treg superenhancer establis...
(A) Analysis of TI Tregs in Figure 4. Treg-specific super-enhancers are associated with Treg signature genes, including Tnfrsf18 (GITR), Tnfrsf4 (OX40), Cxcr4, Tnfrsf9 (4-1BB), Pdcd1 (PD-1), and Icos. (B) Chromosome loops with anchors cobinding with NAT10 and FOXP3 in WT and Nat10-deficient Tregs. Representative Hi-C contact maps at the Cxcr4-containing region in WT and Nat10-deficient Tregs at 5 kb resolution. Blue boxes highlight the local region used for comparison. (C) NAT10-CUT&Tag, FOXP3-CUT&Tag, H3K27ac-CUT&Tag, and ATAC-seq tracks at the Cxcr4 gene locus. (D) qPCR showing the enrichment of FOXP3 at the promoter of Cxcr4 in TI Tregs (n = 4). (E) Representative histogram (left) and quantification of the MFI (right) of CXCR4 in TI Tregs (n = 10). (F) Schematic of the experiment. (G) Representative flow cytometry plot (left) and quantification of the percentages (middle) and number (right) of TI Tregs in lung tumors of the CD45.1 mice adoptively transferred with WT or Nat10-deficient Tregs (n = 8). (H) NAT10-CUT&Tag, FOXP3-CUT&Tag, H3K27ac-CUT&Tag, and ATAC-seq tracks at the Pdcd1 gene locus. (I) qPCR showing the enrichment of FOXP3 at the promoter of Pdcd1 in TI Tregs (n = 4). (J) Representative histogram (left) and quantification of the MFI (right) of PD-1 in TI Tregs (n = 10). (K) NAT10-CUT&Tag, FOXP3-CUT&Tag, H3K27ac-CUT&Tag, and ATAC-seq tracks at the Tnfrsf9 gene locus. (L) qPCR showing the enrichment of FOXP3 at the promoter of Tnfrsf9 in TI Tregs (n = 4). (M) Representative histogram (left) and quantification of the MFI (right) of 4-1BB in TI Tregs (n = 10). Data represent 2–3 independent experiments; mean ± SEM. P values were calculated using 2-tailed unpaired Student’s t test (D, E, G, I, J, L, and M). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.