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Wang L, Zhu M, Li Y, Yan P, Li Z, Chen X, Yang J, Pan X, Zhao H, Wang S, Yuan H, Zhao M, Sun X, Wan R, Li F, Wang X, Yu H, Rosas I, Ding C, Yu G. Serum proteomics identify biomarkers associated with the pathogenesis of idiopathic pulmonary fibrosis. Mol Cell Proteomics 2023; 22:100524. [PMID: 36870568 PMCID: PMC10113895 DOI: 10.1016/j.mcpro.2023.100524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/31/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The heterogeneity of idiopathic pulmonary fibrosis (IPF) limits its diagnosis and treatment. The association between the pathophysiological features and the serum protein signatures of IPF currently remains unclear. The present study analyzed the specific proteins and patterns associated with the clinical parameters of IPF based on a serum proteomic dataset by Data-Independent Acquisition (DIA) using mass spectrometry. Differentiated proteins in sera distinguished in IPF patients into three subgroups in signal pathways and overall survival. Aging-associated signatures by WGCNA coincidently provided clear and direct evidence that aging is a critical risk factor for IPF rather than a single biomarker. LDHA and CCT6A expression, which were associated with glucose metabolic reprogramming, were correlated with high serum lactic acid content in the patients with IPF. Cross-model analysis and machine learning showed that a combinatorial biomarker accurately distinguished IPF patients from healthy subjects with an AUC of 0.848 (95% CI = 0.684-0.941) and validated from another cohort and ELISA assay. This serum proteomic profile provides rigorous evidence that enables understanding of the heterogeneity of IPF and protein alterations that could help in its diagnosis and treatment decisions.
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Affiliation(s)
- Lan Wang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Minghui Zhu
- Henan Provincial Chest Hospital, Zhengzhou, Henan 450003, China
| | - Yan Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Peishuo Yan
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Zhongzheng Li
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xiuping Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Juntang Yang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xin Pan
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Huabin Zhao
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Shenghui Wang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Hongmei Yuan
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Mengxia Zhao
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xiaogang Sun
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Ruyan Wan
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Fei Li
- Henan Provincial Chest Hospital, Zhengzhou, Henan 450003, China
| | - Xiaobo Wang
- Henan Provincial Chest Hospital, Zhengzhou, Henan 450003, China
| | - Hongtao Yu
- Henan Provincial Chest Hospital, Zhengzhou, Henan 450003, China
| | - Ivan Rosas
- Division of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, and School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China.
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan center for outstanding overseas scientists of pulmonary fibrosis, College of Life Sciences, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan 453007, China.
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