Abstract
Polymorphisms of mouse chitinase-like protein 3 (Chil3), a member of the mammalian chitinase-like protein (CLP) family, have been demonstrated to be associated with inflammatory diseases by regulating lipid metabolism. However, the specific immunomodulatory impacts of CLPs, mainly mouse CHIL3 and its human functional homologue chitinase-3-like 2 (CHI3L2), on macrophage cholesterol metabolism and atherosclerosis have remained unclear. Here, we find CLPs (CHIL3 and CHI3L2) accelerate atherogenesis in a macrophage-dependent manner. Mechanistically, we identify an autocrine mechanism through which CLPs regulate cholesterol metabolism in macrophages. Macrophage-secreted CLPs exacerbate lipid uptake by binding to CD36. CLPs exhibit glycosidase activity, targeting and hydrolyzing N-glycosylated glycans on CD36, predominantly at sites N220 and N321, thereby enhancing lipid uptake. Increased lipid influx activates mTOR in macrophages, driving their transition to a pro-inflammatory phenotype while simultaneously suppressing peroxisome proliferator-activated receptor gamma (PPARγ) expression and thus impairing ABCG1-mediated cholesterol efflux. Single-cell sequencing reveals that CLPs increase atherosclerotic foamy macrophages, favoring vascular smooth muscle cells (VSMC) transformation into foam and osteoblast-like cells. Additionally, neutralizing antibodies targeting CHI3L2 prevent and treat atherosclerosis. These findings highlight the potential of CLPs as targets for disease diagnosis and therapy.
Data availability
The raw scRNA-seq data of mouse aortas and the raw RNA-seq data of BMDMs generated in this study have been deposited in the Genome Sequence Archive in National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences, with accession number CRA037644 and CRA037593 that are publicly accessible at https://ngdc.cncb.ac.cn/gsa62,63. The mass spectrometry lipidomics data reported in this paper have been deposited in the OMIX, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (https://ngdc.cncb.ac.cn/omix: accession no. OMIX014576) [https://ngdc.cncb.ac.cn/omix/release/OMIX014576]. The scRNA-seq and RNA-seq datasets used in this study have been previously published and are available in the NCBI Gene Expression Omnibus database under accession numbers GSE15551311, GSE15967722, GSE237219, GSE20741420, GSE2882921, GSE12512624. All data supporting the findings of this study are available within the main text, Supplementary Information or from the corresponding author upon reasonable request. Source data are provided with this paper.
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Acknowledgements
We thank Prof. Baojun Zhang from Xi’an Jiaotong University for the gift of C57BL/6-Ly5.1-Pep3b mice, Prof. Yue Wu from Xi’an Jiaotong University for the help on plasma samples of atherosclerosis patients, Prof. Xiaozhi Zhang from Department of Tumor Radiotherapy of the First Affiliated Hospital of Xi’an Jiaotong University for the help of whole-body X-ray irradiation in mice, and Prof. Feng Guan and Dr. Zengqi Tan from Northwest University for their great help and suggestions on glycosylation study. We are also grateful to Instrumental Analysis Center and Biomedical Experimental Center of Xi’an Jiaotong University for their technical assistance of multiphoton microscope, to Ms. Congcong Xia at Laboratory Animal Center of Xi’an Jiaotong University for her assistance with animal experiment, to LC Bio Technology CO., Ltd for assisting in bulk RNA, scRNA-seq and lipidomic analysis, and to Shanghai Bioprofile Technology for performing the proteomics and quantitative analysis by mass spectrometry for glycomics analyses. We are very grateful for the financial support from the National Natural Science Foundation of China (No. 82370460, WH.Z., 82372900, L.M., 82471830, R.H., W2431021, R.H. and 82171724, WH.Z.), the Natural Science Foundation of Shaanxi (2025JC-JCQN-096, WH.Z., 2025JC-YBMS989, L.M., 2024JC-YBQN-0773, XW.L.), and the Key Research and Development Program of Shaanxi (2024GH-ZDXM-34, L.M.).
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Study design: Y.W., S.L., L.M., R.H., and WH.Z. Animal experiment: Y.W., J.Z., M.F., X.H., WT.Z., W.L., F.L., Y.G., YD.W., B.Y. Cell experiments and molecular biology experiments: Y.W., J.Z., M.F., XM.L., Y.L., YQ.L. scRNA-seq analysis: Y.W. and X.H. H.G., F.N., and X.Z. contributed the human tissue samples. Manuscript drafting: Y.W., XW.L., S.L., L.M., R.H., and WH.Z. All authors contributed to data analysis and interpretation, and manuscript revision.
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The authors declare the following competing interests: A patent application related to the application of CHI3L2 neutralizing antibody in inflammatory diseases has been filed with the China National Intellectual Property Administration by Xi’an Jiaotong University, with WH.Z., F.L., Y.W., L.M., S.L., R.H., and WT.Z. as inventors (application number CN 202511780768.X). The remaining authors declare no competing interests.
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Wang, Y., Zhang, J., Fan, M. et al. Chitinase-like proteins de-N-glycosylating CD36 modify cholesterol metabolism in atherosclerotic macrophages. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71388-x
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DOI: https://doi.org/10.1038/s41467-026-71388-x