Identification and functional validation of lactylation-related hub genes in idiopathic pulmonary fibrosis based on multi-omics analysis
5 affiliations
- 1Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
- 2Department of Respiratory Medicine, Shandong First Medical University Affiliated Provincial Hospital, Jinan, China
- 3Department of Respiratory Medicine, The 958 Hospital of Chinese PLA/Jiangbei Campus, The First Affiliated Hospital of Army Medical University, Chongqing, China
- 4Department of Respiratory Medicine, Sichuan Provincial People’s Hospital, Chengdu, China
- 5Hospital of Jilin University, Changchun, China
Abstract
Background: Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible interstitial lung disease (ILD) characterized by high mortality and poorly understood pathogenesis. Lactylation, a recently identified post-translational modification (PTM), is closely associated with inflammatory responses and tissue fibrosis in various diseases. However, the expression patterns and potential roles of lactylation, as well as the key regulatory genes involved, have not been fully elucidated in IPF. This study aimed to identify lactylation-related hub genes in IPF through bioinformatics analysis and preliminary functional validation, to explore their therapeutic potential, and to evaluate their binding affinity with clinical drugs, providing a theoretical basis for future research on lactylation mechanisms and targeted interventions in IPF.
Methods: Transcriptomic and single-cell sequencing datasets from lung tissues of IPF patients and healthy controls (HC) were obtained from the Gene Expression Omnibus (GEO) database. Weighted Gene Co-expression Network Analysis (WGCNA) was performed to identify IPF-related gene modules. Lactylation-associated hub genes were determined by integrating lactylation-related gene sets with protein-protein interaction (PPI) network analysis. Seurat software and UMAP clustering were employed to identify cell-specific localization of hub genes in lung tissues. Preliminary functional validations, including immunohistochemistry (IHC), Western blotting (WB) for pan-lactylation detection, and gene knockdown assays, were conducted in vitro and in vivo. The CIBERSORT algorithm was applied to analyze immune cell infiltration profiles in IPF tissues. Molecular docking analyses were performed to assess the binding affinity of clinical antifibrotic drugs (pirfenidone and curcumin) with proteins encoded by hub genes.
Results: DDX3X, BCLAF1, and NCL were identified as lactylation-related hub genes in IPF and were specifically expressed in macrophages/neutrophils, ciliated epithelial cells, and lung fibroblasts/macrophages, respectively. The level of pan-lactylation was significantly elevated in IPF lung tissues and TGF-β1-stimulated cellular models. These three hub genes were significantly upregulated in IPF tissues compared with HC, and individual knockdown of each gene significantly inhibited alveolar epithelial-mesenchymal transition (EMT) and human fetal lung fibroblast (HFL1) activation. In addition, these hub genes were closely associated with immune microenvironment remodeling in IPF. Pirfenidone and curcumin demonstrated favorable binding affinity with the proteins encoded by these genes.
Conclusion: The lactylation-related hub genes DDX3X, BCLAF1, and NCL are specifically expressed in distinct cell types within IPF lung tissues, and their upregulation may promote IPF progression by mediating alveolar epithelial EMT, fibroblast activation, and profibrotic immune infiltration, highlighting their potential as therapeutic targets for IPF. Aberrant lactylation activation may contribute to IPF pathogenesis. Pirfenidone and curcumin show promising binding affinity with these hub gene-encoded proteins, providing a theoretical basis for further investigation into lactylation-targeted therapeutic strategies in IPF.
Graphical Abstract:
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12931-026-03783-3.
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BibTeX
@article{yue2026identification,
title = {{Identification and functional validation of lactylation-related hub genes in idiopathic pulmonary fibrosis based on multi-omics analysis}},
author = {Ming Yue and Rumei Luan and Dongyan Ding and Xiao Hu and Jie Tan and Meng Zhao and Lin Zhu and Qianfei Xue and Junling Yang},
journal = {Respiratory Research},
year = {2026},
month = jul,
doi = {10.1186/s12931-026-03783-3},
url = {https://doi.org/10.1186/s12931-026-03783-3},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Identification and functional validation of lactylation-related hub genes in idiopathic pulmonary fibrosis based on multi-omics analysis
AU - Ming Yue
AU - Rumei Luan
AU - Dongyan Ding
AU - Xiao Hu
AU - Jie Tan
AU - Meng Zhao
AU - Lin Zhu
AU - Qianfei Xue
AU - Junling Yang
PY - 2026
DA - 2026/07/04
JO - Respiratory Research
DO - 10.1186/s12931-026-03783-3
UR - https://doi.org/10.1186/s12931-026-03783-3
AB - Background: Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible interstitial lung disease (ILD) characterized by high mortality and poorly understood pathogenesis. Lactylation, a recently identified post-translational modification (PTM), is closely associated with inflammatory responses and tissue fibrosis in various diseases. However, the expression patterns and potential roles of lactylation, as well as the key regulatory genes involved, have not been fully elucidated in IPF. This study aimed to identify lactylation-related hub genes in IPF through bioinformatics analysis and preliminary functional validation, to explore their therapeutic potential, and to evaluate their binding affinity with clinical drugs, providing a theoretical basis for future research on lactylation mechanisms and targeted interventions in IPF. Methods: Transcriptomic and single-cell sequencing datasets from lung tissues of IPF patients and healthy controls (HC) were obtained from the Gene Expression Omnibus (GEO) database. Weighted Gene Co-expression Network Analysis (WGCNA) was performed to identify IPF-related gene modules. Lactylation-associated hub genes were determined by integrating lactylation-related gene sets with protein-protein interaction (PPI) network analysis. Seurat software and UMAP clustering were employed to identify cell-specific localization of hub genes in lung tissues. Preliminary functional validations, including immunohistochemistry (IHC), Western blotting (WB) for pan-lactylation detection, and gene knockdown assays, were conducted in vitro and in vivo. The CIBERSORT algorithm was applied to analyze immune cell infiltration profiles in IPF tissues. Molecular docking analyses were performed to assess the binding affinity of clinical antifibrotic drugs (pirfenidone and curcumin) with proteins encoded by hub genes. Results: DDX3X, BCLAF1, and NCL were identified as lactylation-related hub genes in IPF and were specifically expressed in macrophages/neutrophils, ciliated epithelial cells, and lung fibroblasts/macrophages, respectively. The level of pan-lactylation was significantly elevated in IPF lung tissues and TGF-β1-stimulated cellular models. These three hub genes were significantly upregulated in IPF tissues compared with HC, and individual knockdown of each gene significantly inhibited alveolar epithelial-mesenchymal transition (EMT) and human fetal lung fibroblast (HFL1) activation. In addition, these hub genes were closely associated with immune microenvironment remodeling in IPF. Pirfenidone and curcumin demonstrated favorable binding affinity with the proteins encoded by these genes. Conclusion: The lactylation-related hub genes DDX3X, BCLAF1, and NCL are specifically expressed in distinct cell types within IPF lung tissues, and their upregulation may promote IPF progression by mediating alveolar epithelial EMT, fibroblast activation, and profibrotic immune infiltration, highlighting their potential as therapeutic targets for IPF. Aberrant lactylation activation may contribute to IPF pathogenesis. Pirfenidone and curcumin show promising binding affinity with these hub gene-encoded proteins, providing a theoretical basis for further investigation into lactylation-targeted therapeutic strategies in IPF. Graphical Abstract: Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12931-026-03783-3.
SN - 1465-9921
SN - 1465-993X
ER -