1
|
Bahia W, Soltani I, Abidi A, Mahdhi A, Mastouri M, Ferchichi S, Almawi WY. Structural impact, ligand-protein interactions, and molecular phenotypic effects of TGF-β1 gene variants: In silico analysis with implications for idiopathic pulmonary fibrosis. Gene 2024; 922:148565. [PMID: 38762014 DOI: 10.1016/j.gene.2024.148565] [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: 10/19/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Idiopathic Pulmonary Fibrosis (IPF) is a chronic interstitial lung disease resulting in progressively deteriorating lung function. Transforming growth factor-β1 (TGF-β1) belongs to the TGF superfamily and exerts a profibrotic role in promoting lung fibrosis by facilitating fibroblast infiltration and activity, extracellular matrix deposition, and inhibition of collagen breakdown, thus promoting tissue remodelling and IPF. MATERIALS AND METHODS We evaluated the link between pathogenic TGF-β1 SNPs and IPF pathogenesis and the structure-activity functional consequences of those SNPs on the TGF-β1 protein. Several computational algorithms were merged to address the functional consequences of TGF-β1 gene mutations to protein stability, putative post-translational modification sites, ligand-protein interactions, and molecular phenotypic effects. These included FATHMM, POLYPHEN2, PROVEAN, and SIFT tools (identifying deleterious nsSNPs in the TGF-β1 gene), along with Pmut, PhD-SNP, SNAP, MutPred and the related TMHMM, MARCOIL, and DisProt algorithms (predicting structural disorders). INPS-MD was also used to evaluate the mutation-induced TGF-β1 protein's stability and MODPRED for recognition of post-translational TGF-β1 modification. RESULTS In total, 14 major pathogenic variants markedly impact the destabilization of the TGF-β1 protein, with most of these high-risk mutations associated with decreased stability of the TGF-β1 protein as per the I-Mutant, MUpro, and INPS-MD tools. R205W, R185W, R180Q, D86Y, and I300T variants were proposed to participate in the post-translational modifications, thus affecting affect protein-ligand interactions. Furthermore, at-risk genetic variants appear to target conserved regions in the alpha helices, random coils, and extracellular loops, resulting in a varied composition of amino acids, charge, hydrophobicity, and spatial architecture. CONCLUSIONS This study manuscript comprehensively analyzes gene variants within the TGF-β1 gene, offering novel insights into their structural and functional implications in interacting with target sites. This study is significant for the development of targeted therapeutic strategies and personalized treatment approaches for patients with inflammatory lung diseases such as IPF.
Collapse
Affiliation(s)
- Wael Bahia
- Research Unit of Clinical and Molecular Biology (UR17ES29), Department of Biochemistry, Faculty of Pharmacy of Monastir, University of Monastir, Tunisia
| | - Ismael Soltani
- Research Unit of Clinical and Molecular Biology (UR17ES29), Department of Biochemistry, Faculty of Pharmacy of Monastir, University of Monastir, Tunisia
| | - Anouar Abidi
- Laboratory of Physiology, Faculty of Medicine of Tunis, la Rabta, 1007, Tunis, Tunisia; Laboratory of Functional Physiology and Valorization of Bioresources, High Institute of Biotechnology of Beja, University of Jendouba, Beja, Tunisia
| | - Abdelkarim Mahdhi
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, University of Monastir, Tunisia
| | - Maha Mastouri
- Laboratory of Infectious Diseases and Biological Agents, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Salima Ferchichi
- Research Unit of Clinical and Molecular Biology (UR17ES29), Department of Biochemistry, Faculty of Pharmacy of Monastir, University of Monastir, Tunisia
| | - Wassim Y Almawi
- Faculty of Sciences, El Manar University, Tunis, Tunisia; Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada.
| |
Collapse
|
2
|
Chu L, Zhuo J, Huang H, Chen W, Zhong W, Zhang J, Meng X, Zou F, Cai S, Zou M, Dong H. Tetrandrine alleviates pulmonary fibrosis by inhibiting alveolar epithelial cell senescence through PINK1/Parkin-mediated mitophagy. Eur J Pharmacol 2024; 969:176459. [PMID: 38438063 DOI: 10.1016/j.ejphar.2024.176459] [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: 12/02/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/06/2024]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal and insidious interstitial lung disease. So far, there are no effective drugs for preventing the disease process. Cellular senescence plays a critical role in the development of IPF, with the senescence and insufficient mitophagy of alveolar epithelial cells being implicated in its pathogenesis. Tetrandrine is a natural alkaloid which is now produced synthetically. It was known that the tetrandrine has anti-fibrotic effects, but the efficacy and mechanisms are still not well evaluated. Here, we reveal the roles of tetrandrine on AECs senescence and the antifibrotic effects by using a bleomycin challenged mouse model of pulmonary fibrosis and a bleomycin-stimulated mouse alveolar epithelial cell line (MLE-12). We performed the β-galactosidase staining, immunohistochemistry and fluorescence to assess senescence in MLE-12 cells. The mitophagy levels were detected by co-localization of LC3 and COVIX. Our findings indicate that tetrandrine suppressed bleomycin-induced fibroblast activation and ultimately blocked the increase of collagen deposition in mouse model lung tissue. It has significantly inhibited the bleomycin-induced senescence and senescence-associated secretory phenotype (SASP) in alveolar epithelial cells (AECs). Mechanistically, tetrandrine suppressed the decrease of mitochondrial autophagy-related protein expression to rescue the bleomycin-stimulated impaired mitophagy in MLE-12 cells. We revealed that knockdown the putative kinase 1 (PINK1) gene by a short interfering RNA (siRNA) could abolish the ability of tetrandrine and reverse the MLE-12 cells senescence, which indicated the mitophagy of MLE-12 cells is PINK1 dependent. Our data suggest the tetrandrine could be a novel and effective drug candidate for lung fibrosis and senescence-related fibrotic diseases.
Collapse
Affiliation(s)
- Lanhe Chu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jinzhong Zhuo
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haohua Huang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weimou Chen
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wenshan Zhong
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jinming Zhang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaojing Meng
- School of Public Health, Southern Medical University, Guangzhou, China
| | - Fei Zou
- School of Public Health, Southern Medical University, Guangzhou, China
| | - Shaoxi Cai
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mengchen Zou
- Department of Endocrinology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Hangming Dong
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| |
Collapse
|
3
|
Cala-Garcia JD, Medina-Rincon GJ, Sierra-Salas PA, Rojano J, Romero F. The Role of Mitochondrial Dysfunction in Idiopathic Pulmonary Fibrosis: New Perspectives for a Challenging Disease. BIOLOGY 2023; 12:1237. [PMID: 37759636 PMCID: PMC10525741 DOI: 10.3390/biology12091237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Mitochondrial biology has always been a relevant field in chronic diseases such as fibrosis or cancer in different organs of the human body, not to mention the strong association between mitochondrial dysfunction and aging. With the development of new technologies and the emergence of new methodologies in the last few years, the role of mitochondria in pulmonary chronic diseases such as idiopathic pulmonary fibrosis (IPF) has taken an important position in the field. With this review, we will highlight the latest advances in mitochondrial research on pulmonary fibrosis, focusing on the role of the mitochondria in the aging lung, new proposals for mechanisms that support mitochondrial dysfunction as an important cause for IPF, mitochondrial dysfunction in different cell populations of the lung, and new proposals for treatment of the disease.
Collapse
Affiliation(s)
- Juan David Cala-Garcia
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA;
| | | | | | - Julio Rojano
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92161, USA
| | - Freddy Romero
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA;
| |
Collapse
|
4
|
Chin C, Ravichandran R, Sanborn K, Fleming T, Wheatcroft SB, Kearney MT, Tokman S, Walia R, Smith MA, Flint DJ, Mohanakumar T, Bremner RM, Sureshbabu A. Loss of IGFBP2 mediates alveolar type 2 cell senescence and promotes lung fibrosis. Cell Rep Med 2023; 4:100945. [PMID: 36787736 PMCID: PMC10040381 DOI: 10.1016/j.xcrm.2023.100945] [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: 04/26/2022] [Revised: 06/01/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Abstract
Accumulation of senescent cells contributes to age-related diseases including idiopathic pulmonary fibrosis (IPF). Insulin-like growth factor binding proteins (IGFBPs) regulate many biological processes; however, the functional contributions of IGFBP2 in lung fibrosis remain largely unclear. Here, we report that intranasal delivery of recombinant IGFBP2 protects aged mice from weight loss and demonstrated antifibrotic effects after bleomycin lung injury. Notably, aged human-Igfbp2 transgenic mice reveal reduced senescence and senescent-associated secretory phenotype factors in alveolar epithelial type 2 (AEC2) cells and they ameliorated bleomycin-induced lung fibrosis. Finally, we demonstrate that IGFBP2 expression is significantly suppressed in AEC2 cells isolated from fibrotic lung regions of patients with IPF and/or pulmonary hypertension compared with patients with hypersensitivity pneumonitis and/or chronic obstructive pulmonary disease. Altogether, our study provides insights into how IGFBP2 regulates AEC2-cell-specific senescence and that restoring IGFBP2 levels in fibrotic lungs can prove effective for patients with IPF.
Collapse
Affiliation(s)
- Chiahsuan Chin
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA
| | - Ranjithkumar Ravichandran
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA
| | - Kristina Sanborn
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA
| | - Timothy Fleming
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA
| | - Stephen B Wheatcroft
- Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, Leeds, UK
| | - Mark T Kearney
- Leeds Institute of Cardiovascular & Metabolic Medicine, University of Leeds, Leeds, UK
| | - Sofya Tokman
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA
| | - Rajat Walia
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA
| | - Michael A Smith
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA
| | - David J Flint
- Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Thalachallour Mohanakumar
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA
| | - Ross M Bremner
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA
| | - Angara Sureshbabu
- Norton Thoracic Institute, St. Joseph's Hospital and Medical Center, 124 W. Thomas Road, Ste. 100, Phoenix, AZ 85013, USA; Creighton University School of Medicine - Phoenix Regional Campus, Phoenix, AZ, USA.
| |
Collapse
|
5
|
Cui H, Xie N, Banerjee S, Dey T, Liu RM, Antony VB, Sanders YY, Adams TS, Gomez JL, Thannickal VJ, Kaminski N, Liu G. CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging. Am J Respir Crit Care Med 2022; 206:459-475. [PMID: 35687485 DOI: 10.1164/rccm.202109-2151oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/06/2022] [Indexed: 01/10/2023] Open
Abstract
Rationale: A prevailing paradigm recognizes idiopathic pulmonary fibrosis (IPF) originating from various alveolar epithelial cell (AEC) injuries, and there is a growing appreciation of AEC aging as a key driver of the pathogenesis. Despite this progress, it is incompletely understood what main factor(s) contribute to the worsened alveolar epithelial aging in lung fibrosis. It remains a challenge how to dampen AEC aging and thereby mitigate the disease progression. Objectives: To determine the role of AEC CD38 (cluster of differentiation 38) in promoting cellular aging and lung fibrosis. Methods: We used single-cell RNA sequencing, real-time PCR, flow cytometry, and Western blotting. Measurements and Main Results: We discovered a pivotal role of CD38, a cardinal nicotinamide adenine dinucleotide (NAD) hydrolase, in AEC aging and its promotion of lung fibrosis. We found increased CD38 expression in IPF lungs that inversely correlated with the lung functions of patients. CD38 was primarily located in the AECs of human lung parenchyma and was markedly induced in IPF AECs. Similarly, CD38 expression was elevated in the AECs of fibrotic lungs of young mice and further augmented in those of old mice, which was in accordance with a worsened AEC aging phenotype and an aggravated lung fibrosis in the old animals. Mechanistically, we found that CD38 elevation downregulated intracellular NAD, which likely led to the aging promoting impairment of the NAD-dependent cellular and molecular activities. Furthermore, we demonstrated that genetic and pharmacological inactivation of CD38 improved these NAD dependent events and ameliorated bleomycin-induced lung fibrosis. Conclusions: Our study suggests targeting alveolar CD38 as a novel and effective therapeutic strategy to treat this pathology.
Collapse
Affiliation(s)
- Huachun Cui
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Na Xie
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Sami Banerjee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tapan Dey
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Rui-Ming Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Veena B Antony
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yan Y Sanders
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Taylor S Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Jose L Gomez
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Victor J Thannickal
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Gang Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| |
Collapse
|