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Synthetic polypeptides inhibit nucleic acid-induced inflammation in autoimmune diseases by disrupting multivalent TLR9 binding to LL37-DNA bundles

Abstract

Complexes of extracellular nucleic acids (NAs) with endogenous proteins or peptides, such as LL37, break immune balance and cause autoimmune diseases, whereas NAs with arginine-enriched peptides do not. Inspired by this, we synthesize a polyarginine nanoparticle PEG-TK-NPArg, which effectively inhibits Toll-like receptor-9 (TLR9) activation, in contrast to LL37. To explore the discrepancy effect of PEG-TK-NPArg and LL37, we evaluate the periodic structure of PEG-TK-NPArg-NA and LL37-NA complexes using small-angle X-ray scattering. LL37-NA complexes have a larger inter-NA spacing that accommodates TLR9, while the inter-NA spacing in PEG-TK-NPArg-NA complexes mismatches with the cavity of TLR9, thus inhibiting an interaction with multiple TLR9s, limiting their clustering and damping immune induction. Subsequently, the inhibitory inflammation effect of PEG-TK-NPArg is proved in an animal model of rheumatoid arthritis. This work on how the scavenger-NA complexes inhibit the immune response may facilitate proof-of-concept research translating to clinical application.

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Fig. 1: Synthetic polypeptides inhibiting NA-induced inflammation in RA by disrupting inter-NA spacing to TLR9.
Fig. 2: Cellular toxicity and anti-inflammation efficiency of PEG-TK-NPArg in vitro.
Fig. 3: Nanoparticulate cationic polypeptides showed high DNA binding ability to NCs and effectively inhibited inflammation induced by LL37-NA or HMGB1-NA complexes.
Fig. 4: The inhibitory effect of cationic polypeptides on the interaction between NAs and TLR9.
Fig. 5: Therapeutic and prophylactic efficacies of cationic polypeptide in CIA rats.
Fig. 6: Cationic polypeptides ameliorated joint destruction and elicited a systemic therapeutic response following therapeutic and prophylactic regimens.

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All data supporting the findings of this study are available within the article and Supplementary Information. Source data are provided with this paper.

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Acknowledgements

We thank the financial support from the following funding agencies: the National Natural Science Foundation of China (82341037 to Y.C., 22275213 to L.L., 21875290 to L.L. and 92356310 to Y.Z.), the China Postdoctoral Science Foundation (2023M743133 to X.L. and 2023M743140 to J.H.), the Zhejiang Natural Science Foundation (XHD24E1301 to Y.Z.) and support of Sun Yat-sen University (19lgjc01 to L.L.). We thank S. Cheng (University of Chinese Academy of Sciences (UCAS)) for the support in statistical analysis of data and thank the discussion with D. Yu (Westlake University).

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Contributions

X.L. conducted the main experiments and wrote the paper. S.C. and Y.D. assisted the partial animal studies. J.H. assisted the polypeptide synthesis. Z.L. conducted the SAXS measurement. Y.Z. proposed the multivalent binding mechanism and conducted the SAXS results analysis. L.L. designed and supervised all the experiments and wrote the paper. Y.C. designed and supervised all the experiments and wrote the paper.

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Correspondence to Yue Zhang, Lixin Liu or Yongming Chen.

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Nature Nanotechnology thanks Stefan Bauer and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Biocompatibility of cationic polypeptide in CIA rats.

Systemic toxicity of cationic polypeptide. (a) H&E staining of heart, liver, spleen, lung and kidney samples extracted from normal rats, PBS, PEG-TK-LArg and PEG-TK-NPArg treated CIA rats with established-stage arthritis (the scale bar is 200 μm). (b) ALP, ALT, AST, creatinine, and BUN analysis of established-stage CIA rats at day 29 (n = 3 biologically independent samples). The dash line area is the normal range. The normal ranges of ALP, ALT, and AST are 84 ~ 162, 34.6 ~ 64.0 and 96 ~ 200 U/L, respectively. The normal ranges of creatinine and BUN levels in rat serum are 44.2 ~ 114.9 μmol/L and 9.73 ~ 14.53 mmol/L, respectively. All the quantitative data are presented as mean ± s.d.

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Liu, X., Chen, S., Huang, J. et al. Synthetic polypeptides inhibit nucleic acid-induced inflammation in autoimmune diseases by disrupting multivalent TLR9 binding to LL37-DNA bundles. Nat. Nanotechnol. 19, 1745–1756 (2024). https://doi.org/10.1038/s41565-024-01759-2

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