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Lou YX, Shi ED, Yang R, Yang Y. Exploring the mechanisms of glycolytic genes involvement in pulmonary arterial hypertension through integrative bioinformatics analysis. J Cell Mol Med 2024; 28:e18447. [PMID: 38837574 DOI: 10.1111/jcmm.18447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/17/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024] Open
Abstract
The purpose of this study was to identify the mechanisms underlying the involvement of glycolytic genes in pulmonary arterial hypertension (PAH). This study involved downloading 3 datasets from the GEO database at the National Center for Biotechnology Information. The datasets were processed to obtain expression matrices for analysis. Genes involved in glycolysis-related pathways were obtained, and genes related to glycolysis were selected based on significant differences in expression. Gene Ontology functional annotation analysis, Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and GSEA enrichment analysis were performed on the DEGs. Combining LASSO regression with SVM-RFE machine learning technology, a PAH risk prediction model based on glycolysis related gene expression was constructed, and CIBERSORTx technology was used to analyse the immune cell composition of PAH patients. Gene enrichment analysis revealed that the DEGs work synergistically across multiple biological pathways. A total of 6 key glycolysis-related genes were selected using LASSO regression and SVM. A bar plot was constructed to evaluate the weights of the key genes and predict the risk of PAH. The clinical application value and predictive accuracy of the model were assessed. Immunological feature analysis revealed significant correlations between key glycolysis-related genes and the abundances of different immune cell types. The glycolysis genes (ACSS2, ALAS2, ALDH3A1, ADOC3, NT5E, and TALDO1) identified in this study play important roles in the development of pulmonary arterial hypertension, providing new evidence for the involvement of glycolysis in PAH.
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Affiliation(s)
- Yu-Xuan Lou
- Department of cardiology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Er-Dan Shi
- Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People's Republic of China
| | - Rong Yang
- Department of Rheumatology and Immunology, Zhongda Hospital Affiliated to Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Yang Yang
- Department of cardiology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
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Liao Y, Yang Y, Zhou G, Chen L, Yang Y, Guo S, Zuo Q, Zou J. Anoikis and SPP1 in idiopathic pulmonary fibrosis: integrating bioinformatics, cell, and animal studies to explore prognostic biomarkers and PI3K/AKT signaling regulation. Expert Rev Clin Immunol 2024; 20:679-693. [PMID: 38318669 DOI: 10.1080/1744666x.2024.2315218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/01/2024] [Indexed: 02/07/2024]
Abstract
OBJECTIVE This study aims to explore the relevance of anoikis in idiopathic pulmonary fibrosis (IPF) and identify associated biomarkers and signaling pathways. METHOD Unsupervised consensus cluster analysis was employed to categorize IPF patients into subtypes. We utilized Weighted Gene Co-Expression Network Analysis (WGCNA) and Protein-Protein Interaction network construction to identify anoikis-related modules and key genes. A prognostic signature was developed using Lasso and multivariate Cox regression analysis. Single-cell sequencing assessed hub gene expression in various cell types, and both cell and animal experiments confirmed IPF-related pathways. RESULTS We identified two distinct anoikis-associated subtypes with differing prognoses. WGCNA revealed essential hub genes, with SPP1 being prominent in the anoikis-related signature. The anoikis-related signature is effective in determining the prognosis of patients with IPF. Single-cell sequencing highlighted significant differences in SPP1 expression, notably elevated in fibroblasts derived from IPF patients. In vivo and in vitro experiments demonstrated that SPP1 enhances fibrosis in mouse lung fibroblasts by regulating p27 through the PI3K/Akt pathway. CONCLUSION Our research demonstrates a robust prognostic signature associated with anoikis and highlights SPP1 as a pivotal regulator of the PI3K/AKT signaling pathway in pulmonary fibrosis.
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Affiliation(s)
- Yi Liao
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Yang
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Guanghong Zhou
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lijuan Chen
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yang Yang
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shujin Guo
- Department of Health Management & Institute of Health Management, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Qiunan Zuo
- Department of Geriatric Respiratory, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jun Zou
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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Iturbe-Fernández D, Pulito-Cueto V, Mora-Cuesta VM, Remuzgo-Martínez S, Ferrer-Pargada DJ, Genre F, Alonso-Lecue P, López-Mejías R, Atienza-Mateo B, González-Gay MA, Cifrián-Martínez JM. Osteopontin as a Biomarker in Interstitial Lung Diseases. Biomedicines 2024; 12:1108. [PMID: 38791069 PMCID: PMC11118604 DOI: 10.3390/biomedicines12051108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Osteopontin (OPN) is a glycoprotein involved in Th1 and Th17 differentiation, and inflammation and tissue remodeling. OPN is a biomarker of disease activity in patients with autoimmune inflammatory conditions. This study aimed to assess the diagnostic and prognostic value of OPN in interstitial lung diseases (ILDs). Between May 2016 and October 2019, 344 patients with ILD were recruited at the Hospital Universitario Marqués de Valdecilla (Spain) and were prospectively followed-up. This study involved the determination of OPN serum levels by ELISA and OPN RNA expression quantified using qPCR. Six genetic polymorphisms in OPN (rs28357094, rs2853749, rs2853750, rs11728697, rs7695531, and rs1126616) were genotyped using TaqMan assays. OPN serum levels were also assessed in 140 healthy controls. OPN serum levels (median [interquartile range]) were significantly higher in ILD patients than in controls (1.05 [0.75-1.51] ng/mL versus 0.81 [0.65-0.98] ng/mL in healthy controls; p < 0.01). OPN serum levels were inversely correlated with the forced vital capacity. OPN serum levels were also higher in ILD patients who died or underwent lung transplantation when compared with the remaining ILD patients (1.15 [0.80-1.72] ng/mL versus 0.99 [0.66-1.32] ng/mL; p = 0.05). Survival worsened in ILD patients with OPN > 1.03 ng/mL at 1, 3, and 5 years. No statistically significant differences in the genetic frequencies of OPN polymorphisms or the RNA expression were found among the different ILD groups. Elevated levels of OPN in the serum may be a useful indicator in identifying patients with ILD who are more likely to experience poor outcomes.
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Affiliation(s)
- David Iturbe-Fernández
- Pneumology Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain; (V.M.M.-C.); (D.J.F.-P.)
| | - Verónica Pulito-Cueto
- Valdecilla Research Institute (IDIVAL), 39008 Santander, Spain; (V.P.-C.); (S.R.-M.); (F.G.); (P.A.-L.); (R.L.-M.); (B.A.-M.)
| | - Víctor M. Mora-Cuesta
- Pneumology Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain; (V.M.M.-C.); (D.J.F.-P.)
| | - Sara Remuzgo-Martínez
- Valdecilla Research Institute (IDIVAL), 39008 Santander, Spain; (V.P.-C.); (S.R.-M.); (F.G.); (P.A.-L.); (R.L.-M.); (B.A.-M.)
| | - Diego J. Ferrer-Pargada
- Pneumology Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain; (V.M.M.-C.); (D.J.F.-P.)
| | - Fernanda Genre
- Valdecilla Research Institute (IDIVAL), 39008 Santander, Spain; (V.P.-C.); (S.R.-M.); (F.G.); (P.A.-L.); (R.L.-M.); (B.A.-M.)
| | - Pilar Alonso-Lecue
- Valdecilla Research Institute (IDIVAL), 39008 Santander, Spain; (V.P.-C.); (S.R.-M.); (F.G.); (P.A.-L.); (R.L.-M.); (B.A.-M.)
| | - Raquel López-Mejías
- Valdecilla Research Institute (IDIVAL), 39008 Santander, Spain; (V.P.-C.); (S.R.-M.); (F.G.); (P.A.-L.); (R.L.-M.); (B.A.-M.)
| | - Belén Atienza-Mateo
- Valdecilla Research Institute (IDIVAL), 39008 Santander, Spain; (V.P.-C.); (S.R.-M.); (F.G.); (P.A.-L.); (R.L.-M.); (B.A.-M.)
- Division of Rheumatology, Marqués de Valdecilla University Hospital, 39008 Santander, Spain
| | - Miguel A. González-Gay
- Medicine and Psychiatry Department, University of Cantabria, 39005 Santander, Spain;
- Division of Rheumatology, IIS-Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - José M. Cifrián-Martínez
- Pneumology Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain; (V.M.M.-C.); (D.J.F.-P.)
- Valdecilla Research Institute (IDIVAL), 39008 Santander, Spain; (V.P.-C.); (S.R.-M.); (F.G.); (P.A.-L.); (R.L.-M.); (B.A.-M.)
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Hu W, Xu Y. Transcriptomics in idiopathic pulmonary fibrosis unveiled: a new perspective from differentially expressed genes to therapeutic targets. Front Immunol 2024; 15:1375171. [PMID: 38566986 PMCID: PMC10985171 DOI: 10.3389/fimmu.2024.1375171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Background The underlying molecular pathways of idiopathic pulmonary fibrosis (IPF), a progressive lung condition with a high death rate, are still mostly unknown. By using microarray datasets, this study aims to identify new genetic targets for IPF and provide light on the genetic factors that contribute to the development of IPF. Method We conducted a comprehensive analysis of three independent IPF datasets from the Gene Expression Omnibus (GEO) database, employing R software for data handling and normalization. Our evaluation of the relationships between differentially expressed genes (DEGs) and IPF included differential expression analysis, expression quantitative trait loci (eQTL) analysis, and Mendelian Randomization(MR) analyses. Additionally, we used Gene Set Enrichment Analysis (GSEA) and Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to explore the functional roles and pathways of these genes. Finally, we validated the results obtained for the target genes. Results We identified 486 highly expressed genes and 468 lowly expressed genes that play important roles in IPF. MR analysis identified six significantly co-expressed genes associated with IPF, specifically C12orf75, SPP1, ZG16B, LIN7A, PPP1R14A, and TLR2. These genes participate in essential biological processes and pathways, including macrophage activation and neural system regulation. Additionally, CIBERSORT analysis indicated a unique immune cell distribution in IPF, emphasized the significance of immunological processes in the disease. The MR analysis was consistent with the results of the analysis of variance in the validation cohort, which strengthens the reliability of our MR findings. Conclusion Our findings provide new insights into the molecular basis of IPF and highlight the promise of therapeutic interventions. They emphasize the potential of targeting specific molecular pathways for the treatment of IPF, laying the foundation for further research and clinical work.
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Affiliation(s)
- Wenzhong Hu
- Guang’anmen Hospital South Campus, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yun Xu
- People's Hospital of Beijing Daxing District, Capital Medical University, Beijing, China
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Zhu X, Ji J, Han X. Osteopontin: an essential regulatory protein in idiopathic pulmonary fibrosis. J Mol Histol 2024; 55:1-13. [PMID: 37878112 DOI: 10.1007/s10735-023-10169-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, chronic lung disease characterized by abnormal proliferation and activation of fibroblasts, excessive accumulation of extracellular matrix (ECM), inflammatory damage, and disrupted alveolar structure. Despite its increasing morbidity and mortality rates, effective clinical treatments for IPF remain elusive. Osteopontin (OPN), a multifunctional ECM protein found in various tissues, has been implicated in numerous biological processes such as bone remodeling, innate immunity, acute and chronic inflammation, and cancer. Recent studies have highlighted the pivotal role of OPN in the pathogenesis of IPF. This review aims to delve into the involvement of OPN in the inflammatory response, ECM deposition, and epithelial-mesenchymal transition (EMT) during IPF, and intends to lay a solid theoretical groundwork for the development of therapeutic strategies for IPF.
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Affiliation(s)
- Xiaoyu Zhu
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Hankou Road 22, Nanjing, 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210093, China
| | - Jie Ji
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Hankou Road 22, Nanjing, 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210093, China
| | - Xiaodong Han
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Hankou Road 22, Nanjing, 210093, China.
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210093, China.
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Tang Z, Xia Z, Wang X, Liu Y. The critical role of osteopontin (OPN) in fibrotic diseases. Cytokine Growth Factor Rev 2023; 74:86-99. [PMID: 37648616 DOI: 10.1016/j.cytogfr.2023.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
Fibrosis is a pathological condition characterized by the excessive deposition of extracellular matrix components in tissues and organs, leading to progressive architectural remodelling and contributing to the development of various diseases. Osteopontin (OPN), a highly phosphorylated glycoprotein, has been increasingly recognized for its involvement in the progression of tissue fibrosis. This review provides a comprehensive overview of the genetic and protein structure of OPN and focuses on our current understanding of the role of OPN in the development of fibrosis in the lungs and other tissues. Additionally, special attention is given to the potential of OPN as a biomarker and a novel therapeutic target in the treatment of fibrosis.
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Affiliation(s)
- Ziyi Tang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Laboratory of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zijing Xia
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Laboratory of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiangpeng Wang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100000, China
| | - Yi Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Laboratory of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China; Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
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Karampitsakos T, Juan-Guardela BM, Tzouvelekis A, Herazo-Maya JD. Precision medicine advances in idiopathic pulmonary fibrosis. EBioMedicine 2023; 95:104766. [PMID: 37625268 PMCID: PMC10469771 DOI: 10.1016/j.ebiom.2023.104766] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/07/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a highly heterogeneous, unpredictable and ultimately lethal chronic lung disease. Over the last decade, two anti-fibrotic agents have been shown to slow disease progression, however, both drugs are administered uniformly with minimal consideration of disease severity and inter-individual molecular, genetic, and genomic differences. Advances in biological understanding of disease endotyping and the emergence of precision medicine have shown that "a one-size-fits-all approach" to the management of chronic lung diseases is no longer appropriate. While precision medicine approaches have revolutionized the management of other diseases such as lung cancer and asthma, the implementation of precision medicine in IPF clinical practice remains an unmet need despite several reports demonstrating a large number of diagnostic, prognostic and theragnostic biomarker candidates in IPF. This review article aims to summarize our current knowledge of precision medicine in IPF and highlight barriers to translate these research findings into clinical practice.
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Affiliation(s)
- Theodoros Karampitsakos
- Division of Pulmonary, Critical Care and Sleep Medicine, Ubben Center for Pulmonary Fibrosis Research, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Brenda M Juan-Guardela
- Division of Pulmonary, Critical Care and Sleep Medicine, Ubben Center for Pulmonary Fibrosis Research, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | | | - Jose D Herazo-Maya
- Division of Pulmonary, Critical Care and Sleep Medicine, Ubben Center for Pulmonary Fibrosis Research, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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