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Meshkovska Y, Dzhuraeva B, Godugu C, Pooladanda V, Thatikonda S. Deciphering the interplay: circulating cell-free DNA, signaling pathways, and disease progression in idiopathic pulmonary fibrosis. 3 Biotech 2025; 15:102. [PMID: 40165930 PMCID: PMC11954786 DOI: 10.1007/s13205-025-04272-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 03/10/2025] [Indexed: 04/02/2025] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a lung disease with an unknown etiology and a short survival rate. There is no accurate method of early diagnosis, and it involves computed tomography (CT) or lung biopsy. Since diagnostic methods are not accurate due to their similarity to other lung pathologies, discovering new biomarkers is a key issue for diagnosticians. Currently, the use of ccf-DNA (circulating cell-free deoxyribonucleic acid) is an important focus due to its association with IPF-induced alterations in metabolic pathways, such as amino acid metabolism, energy metabolism, and lipid metabolism pathways. Other biomarkers associated with metabolic changes have been found, and they are related to changes in type II/type I alveolar epithelial cells (AECs I/II), changes in extracellular matrix (ECM), and inflammatory processes. Currently, IPF pathogenetic treatment remains unknown, and the mortality rates are increasing, and the patients are diagnosed at a late stage. Signaling pathways and metabolic dysfunction have a significant role in the disease occurrence, particularly the transforming growth factor-β (TGF-β) signaling pathway, which plays an essential role. TGF-β, Wnt, Hedgehog (Hh), and integrin signaling are the main drivers of fibrosis. These pathways activate the transformation of fibroblasts into myofibroblasts, extracellular matrix (ECM) deposition, and tissue remodeling fibrosis. Therapy targeting diverse signaling pathways to slow disease progression is crucial in the treatment of IPF. Two antifibrotic medications, including pirfenidone and nintedanib, are Food and Drug Administration (FDA)-approved for treatment. ccf-DNA could become a new biomarker for IPF diagnosis to detect the disease at the early stage, while FDA-approved therapies could help to prevent late conditions from forming and decrease mortality rates.
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Affiliation(s)
- Yeva Meshkovska
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL 33612 USA
| | - Barchinai Dzhuraeva
- Department of Hospital Pediatrics, Moffitt Cancer Center, Tampa, FL 33612 USA
- Department of Hospital Pediatrics with a Course of Neonatology, National Center of Maternal and Child Health, Bishkek, 720017 Kyrgyzstan
| | - Chandraiah Godugu
- Department of Regulatory Toxicology, Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037 India
| | - Venkatesh Pooladanda
- Vincent Center for Reproductive Biology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, 60 Blossom Street, Thier 9, Boston, MA 02114 USA
- Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA 02115 USA
| | - Sowjanya Thatikonda
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL 33612 USA
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Balnadupete A, Moideen FM, Varughese A, Mugaranja K, M JT, Charavu R, Bhandary Y. Beyond the pill: incrimination of nuclear factor-kappa B and their targeted phytomedicine for pulmonary fibrosis. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025:10.1007/s00210-025-04067-1. [PMID: 40137966 DOI: 10.1007/s00210-025-04067-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/01/2025] [Accepted: 03/17/2025] [Indexed: 03/29/2025]
Abstract
Pulmonary fibrosis (PF) is a slow and irreparable damage of the lung caused by the accumulation of scar tissue, which eventually results in organ dysfunction and fatality from gas exchange failure. One of the extensively studied inflammatory pathways in PF is the NF-κB signalling pathway, which is reportedly involved in epithelial-mesenchymal transition, myofibroblast differentiation, and other cellular processes. Additionally, studies have evidence that NF-κB signalling pathways can be employed as a potential target for developing therapeutic agents against PF. In the current scenario, FDA-approved drugs, nintedanib and pirfenidone, have been used for the treatment of PF with potential side effects. Recently, the usage of bioactive compounds has attracted attention in the treatment of PF. This review focuses on the involvement of the NF-κB signalling pathway in PF and the significance of phytocompounds in regulating the NF-κB pathway. Both the in vitro and in vivo studies reveal that NF-κB-targeted plant-based bioactive compounds significantly ameliorate the PF condition as well as improve the health condition. Databases such as Scopus, PubMed, and Web of Science were used to conduct literature surveys and compile data on all the bioactive compounds. In conclusion, the plant-derived bioactive compounds are potent enough to target the NF-κB with its biological properties, and this could be a highly effective therapeutic strategy for PF in the future.
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Affiliation(s)
- Akarsha Balnadupete
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India
| | - Fathimath Muneesa Moideen
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India
| | - Aleena Varughese
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India
| | - Kirana Mugaranja
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India
| | - Jeena T M
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India
| | - Rakshitha Charavu
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India
| | - Yashodhar Bhandary
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India.
- Specialized Research Unit, Yenepoya Medical College & Hospital, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, Karnataka, 575018, India.
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Corrêa RO, Castro PR, Moser R, Ferreira CM, Quesniaux VFJ, Vinolo MAR, Ryffel B. Butyrate: Connecting the gut-lung axis to the management of pulmonary disorders. Front Nutr 2022; 9:1011732. [PMID: 36337621 PMCID: PMC9631819 DOI: 10.3389/fnut.2022.1011732] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022] Open
Abstract
Short-chain fatty acids (SCFAs) are metabolites released by bacterial components of the microbiota. These molecules have a wide range of effects in the microbiota itself, but also in host cells in which they are known for contributing to the regulation of cell metabolism, barrier function, and immunological responses. Recent studies indicate that these molecules are important players in the gut-lung axis and highlight the possibility of using strategies that alter their intestinal production to prevent or treat distinct lung inflammatory diseases. Here, we review the effects of the SCFA butyrate and its derivatives in vitro and in vivo on murine models of respiratory disorders, besides discussing the potential therapeutic use of butyrate and the other SCFAs in lung diseases.
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Affiliation(s)
- Renan Oliveira Corrêa
- Laboratory of Immunoinflammation, Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Laboratory of Intestinal Immunology, Institut Imagine, INSERM U1163, Paris, France
| | - Pollyana Ribeiro Castro
- Laboratory of Immunoinflammation, Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Caroline Marcantonio Ferreira
- Department of Pharmaceutics Science, Institute of Environmental, Chemistry, and Pharmaceutical Sciences, Federal University of São Paulo, Diadema, Brazil
| | | | - Marco Aurélio Ramirez Vinolo
- Laboratory of Immunoinflammation, Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster, Institute of Biology, University of Campinas, Campinas, Brazil
- Center for Research on Obesity and Comorbidities, University of Campinas, Campinas, Brazil
- *Correspondence: Marco Aurélio Ramirez Vinolo,
| | - Bernhard Ryffel
- CNRS, INEM, UMR 7355, University of Orléans, Orléans, France
- Bernhard Ryffel,
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Hao MJ, Chen PN, Li HJ, Wu F, Zhang GY, Shao ZZ, Liu XP, Ma WZ, Xu J, Mahmud T, Lan WJ. β-Carboline Alkaloids From the Deep-Sea Fungus Trichoderma sp. MCCC 3A01244 as a New Type of Anti-pulmonary Fibrosis Agent That Inhibits TGF-β/Smad Signaling Pathway. Front Microbiol 2022; 13:947226. [PMID: 35966687 PMCID: PMC9366743 DOI: 10.3389/fmicb.2022.947226] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022] Open
Abstract
Pulmonary fibrosis is a scarring disease of lung tissue, which seriously threatens human health. Treatment options are currently limited, and effective strategies are still lacking. In the present study, 25 compounds were isolated from the deep-sea fungus Trichoderma sp. MCCC 3A01244. Among them, two β-carboline alkaloids, trichocarbolines A (1) and C (4) are new compounds. The chemical structures of these compounds were elucidated based on their HRESIMS, 1D and 2D NMR spectra, optical rotation calculation, and comparisons with data reported in the literature. Trichocarboline B [(+)- and (–)-enantiomers] had previously been synthesized, and this is its first report as a natural product. Their anti-pulmonary fibrosis (PF) activity and cytotoxicity were investigated. Compounds 1, 11, and 13 strongly inhibited TGF-β1-induced total collagen accumulation and showed low cytotoxicity against the HFL1 cell line. Further studies revealed compound 1 inhibited extracellular matrix (ECM) deposition by downregulating the expression of protein fibronectin (FN), proliferating cell nuclear antigen (PCNA), and α-smooth muscle actin (α-SMA). Mechanistic study revealed that compound 1 decreased pulmonary fibrosis by inhibiting the TGF-β/Smad signaling pathway. As a newly identified β-carboline alkaloid, compound 1 may be used as a lead compound for developing more efficient anti-pulmonary fibrosis agents.
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Affiliation(s)
- Meng-Jiao Hao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Pei-Nan Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hou-Jin Li
- School of Chemistry, Sun Yat-sen University, Guangzhou, China
| | - Feng Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Guang-Yu Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zong-Ze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiu-Pian Liu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Wen-Zhe Ma
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Jun Xu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, United States
| | - Wen-Jian Lan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Wen-Jian Lan,
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Elias M, Zhao S, Le HT, Wang J, Neurath MF, Neufert C, Fiocchi C, Rieder F. IL-36 in chronic inflammation and fibrosis - bridging the gap? J Clin Invest 2021; 131:144336. [PMID: 33463541 DOI: 10.1172/jci144336] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
IL-36 is a member of the IL-1 superfamily and consists of three agonists and one receptor antagonist (IL-36Ra). The three endogenous agonists, IL-36α, -β, and -γ, act primarily as proinflammatory cytokines, and their signaling through the IL-36 receptor (IL-36R) promotes immune cell infiltration and secretion of inflammatory and chemotactic molecules. However, IL-36 signaling also fosters secretion of profibrotic soluble mediators, suggesting a role in fibrotic disorders. IL-36 isoforms and IL-36 have been implicated in inflammatory diseases including psoriasis, arthritis, inflammatory bowel diseases, and allergic rhinitis. Moreover, IL-36 has been connected to fibrotic disorders affecting the kidney, lung, and intestines. This review summarizes the expression, cellular source, and function of IL-36 in inflammation and fibrosis in various organs, and proposes that IL-36 modulation may prove valuable in preventing or treating inflammatory and fibrotic diseases and may reveal a mechanistic link between inflammation and fibrosis.
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Affiliation(s)
- Michael Elias
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Shuai Zhao
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Hongnga T Le
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jie Wang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Henan Key Laboratory of Immunology and Targeted Drug, Xinxiang Medical University, Xinxiang, Henan Province, China
| | - Markus F Neurath
- Department of Medicine 1 and Deutsches Zentrum Immuntherapie DZI, Universitaetsklinikum Erlangen, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Clemens Neufert
- Department of Medicine 1 and Deutsches Zentrum Immuntherapie DZI, Universitaetsklinikum Erlangen, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Claudio Fiocchi
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Florian Rieder
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Diseases and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
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