1
|
He J, Hu J, Liu H. A three-gene random forest model for diagnosing idiopathic pulmonary fibrosis based on circadian rhythm-related genes in lung tissue. Expert Rev Respir Med 2023; 17:1307-1320. [PMID: 38285622 DOI: 10.1080/17476348.2024.2311262] [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: 12/13/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND The disorder of circadian rhythm could be a key factor mediating fibrotic lung disease Therefore, our study aims to determine the diagnostic value of circadian rhythm-related genes (CRRGs) in IPF. METHODS We retrieved the data on CRRGs from previous studies and the GSE150910 dataset. The participants from the GSE150910 dataset were divided into training and internal validation sets. Next, we used several various bioinformatics methods and machine learning algorithms to screen genes. Next, we identified SEMA5A, COL7A1, and TUBB3, which were included in the random forest (RF) diagnostic model. Finally, external validation was conducted on data retrieved from the GSE184316 datasets. RESULTS The results revealed that the RF diagnostic model could diagnose patients with IPF in the internal validation set with the area under the ROC curve (AUC) value of 0.905 and in the external validation with the AUC value of 0.767. Furthermore, real-time quantitative PCR and western blotting results revealed a significant decrease in SEMA5A (p < 0.05) expression level and an increase in COL7A1 and TUBB3 expression levels in TGF-β1-treated normal human lung fibroblasts. CONCLUSION We constructed an RF diagnostic model based on SEMA5A, COL7A1, and TUBB3 expression in lung tissue for diagnosing patients with IPF.
Collapse
Affiliation(s)
- Jie He
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Hu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Otolaryngology - Head and Neck Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Hairong Liu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Geriatric Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| |
Collapse
|
2
|
Therapeutic Potential of Ajwa Dates (Phoenix dactylifera) Extract in Prevention of Benzo(a)pyrene-Induced Lung Injury through the Modulation of Oxidative Stress, Inflammation, and Cell Signalling Molecules. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12136784] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Chronic respiratory diseases are a leading cause of lung-related death worldwide. The vital factors causing lung pathogenesis include consistent exposure to tobacco smoke, air pollution, and occupational risks. Regarding the significant morbidity and mortality linked to lung pathogenesis, there are neither conclusive treatments nor wholly preventive strategies. In the present study, the protective mechanism of Ajwa date extract (ADE), on Benzopyrene [B(a)P]-induced lung injury in animal models was investigated using antioxidant, lipid peroxidation, anti-inflammatory activities, angiogenesis, histopathological studies, and apoptosis assays. B(a)P treatment significantly decreased the level of antioxidant enzymes such as catalase (Cat) (13.4 vs. 24.7 U/mg protein), Superoxide dismutase (SOD) (38.5 vs. 65.7 U/mg protein), Glutathione peroxidase (GPx) (42.4 vs. 57.3 U/mg protein) and total antioxidant capacity (TAC) (49.8 vs. 98.7 nM) as compared to the treatment group (p < 0.05). B(a)P treatment led to increased expression of pro-inflammatory markers such as TNF-α (88.5 vs. 72.6 pg/mL), IFN-γ (4.86 vs. 3.56 pg/mL), interleukin-6 (IL-6) (109.6 vs. 85.4 pg/mL) and CRP (1.84 vs. 0.94 ng/mL) as compared to the treatment group (p < 0.05). The data shows a significant increase in lipid peroxidation and angiogenesis factors such as vascular endothelial growth factor (VEGF) by B(a)P treatment (p < 0.05). However, ADE treatment showed an improvement of these factors. In addition, ADE treatment significantly ameliorated histopathological changes, collagen fiber deposition, and expression pattern of VEGF and Bax proteins. Furthermore, the flow cytometry data demonstrated that B(a)P intoxication enhanced the apoptosis ratio, which was significantly improved with ADE treatment. Finally, we may infer that Phyto-constituents of ADE have the potential to protect against B(a)P-induced lung pathogenesis. Therefore, Ajwa dates might be used to develop a possible potent alternative therapy for lung pathogenesis.
Collapse
|
3
|
Miller KN, Victorelli SG, Salmonowicz H, Dasgupta N, Liu T, Passos JF, Adams PD. Cytoplasmic DNA: sources, sensing, and role in aging and disease. Cell 2021; 184:5506-5526. [PMID: 34715021 PMCID: PMC8627867 DOI: 10.1016/j.cell.2021.09.034] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/17/2022]
Abstract
Endogenous cytoplasmic DNA (cytoDNA) species are emerging as key mediators of inflammation in diverse physiological and pathological contexts. Although the role of endogenous cytoDNA in innate immune activation is well established, the cytoDNA species themselves are often poorly characterized and difficult to distinguish, and their mechanisms of formation, scope of function and contribution to disease are incompletely understood. Here, we summarize current knowledge in this rapidly progressing field with emphases on similarities and differences between distinct cytoDNAs, their underlying molecular mechanisms of formation and function, interactions between cytoDNA pathways, and therapeutic opportunities in the treatment of age-associated diseases.
Collapse
Affiliation(s)
- Karl N Miller
- Aging, Cancer and Immuno-oncology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Stella G Victorelli
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Hanna Salmonowicz
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA; Institute for Cell and Molecular Biosciences & Newcastle University Institute for Ageing, Newcastle upon Tyne NE4 5PL, UK; International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, 02-109 Warsaw, Poland
| | - Nirmalya Dasgupta
- Aging, Cancer and Immuno-oncology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Tianhui Liu
- Aging, Cancer and Immuno-oncology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - João F Passos
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA.
| | - Peter D Adams
- Aging, Cancer and Immuno-oncology Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
4
|
Ke S, Zhang Y, Lan Z, Li S, Zhu W, Liu L. Curcumin protects murine lung mesenchymal stem cells from H 2O 2 by modulating the Akt/Nrf2/HO-1 pathway. J Int Med Res 2021; 48:300060520910665. [PMID: 32237999 PMCID: PMC7132811 DOI: 10.1177/0300060520910665] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Objectives Oxidative stress within the idiopathic pulmonary fibrosis microenvironment decreases the survival of lung mesenchymal stem cells (LMSCs), resulting in disease progression. Herein, the effects of curcumin (CUR) against hydrogen peroxide (H2O2)-mediated damage to murine LMSCs were examined. Methods Apoptosis, reactive oxygen species, and mitochondrial membrane potential were detected by flow cytometry. Protein levels of B-cell lymphoma-2 (Bcl-2), Bcl-2 associated x (Bax), cleaved caspase-3, protein kinase B (PKB/Akt), phosphorylated-Akt, nuclear factor erythroid-2-related factor 2 (Nrf2), and heme oxygenase-1 (HO-1) were evaluated by western blot analysis. Results Apoptosis rates in the 2.5, 5, and 10 µM CUR groups were 23.27% ± 0.31%, 14.87% ±0.41%, and 6.47% ± 0.50%, respectively, all of which were lower than in the H2O2 group (24.46% ± 1.35%). Reactive oxygen species levels were decreased, while mitochondrial membrane potential levels were increased in concentration-dependent manners in the CUR groups compared with the H2O2 group. Compared with the H2O2 group, all CUR groups showed reduced cleaved caspase-3 expression, increased Nrf2 and HO-1 expression, and increased Bcl-2/Bax and p-Akt/Akt ratios. Conclusions The protective effects of CUR against H2O2-mediated damage in murine LMSCs may be mediated through the Akt/Nrf2/HO-1 signaling pathway.
Collapse
Affiliation(s)
- Shiwen Ke
- School of Clinical Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| | - Yuanbing Zhang
- Department of Respiration, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| | - Zhihui Lan
- Department of Respiration, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| | - Shaofeng Li
- Department of Respiration, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| | - Wei Zhu
- The Second Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Liangji Liu
- Department of Respiration, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, China
| |
Collapse
|
5
|
Muthuramalingam K, Cho M, Kim Y. Cellular senescence and EMT crosstalk in bleomycin-induced pathogenesis of pulmonary fibrosis-an in vitro analysis. Cell Biol Int 2019; 44:477-487. [PMID: 31631444 DOI: 10.1002/cbin.11248] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Abstract
With poor prognosis and aberrant lung remodeling, pulmonary fibrosis exhibits worldwide prevalence accompanied by an increase in burden in terms of hospitalization and death. Apart from genetic and non-genetic factors, fibrosis occurs as a side effect of bleomycin antineoplastic activity. Elucidating the cellular and molecular mechanism could help in the development of effective anti-fibrotic treatment strategies. In the present study, we investigated the underlying mechanism behind bleomycin-induced fibrosis using human alveolar epithelial cells (A549 cells). On the basis of the experimental observation, it was demonstrated that with transforming growth factor-β (TGF-β) as a central mediator of fibrosis progression, a cross-talk between epithelial-mesenchymal transition (EMT) and senescence upon bleomycin treatment occurs. This results in the advancement of this serious fibrotic condition. Fibrosis was initiated through integrin activation and imbalance in the redox state (NOX expression) of the cell. It progressed along the TGF-β-mediated non-canonical pathway (via ERK phosphorylation) followed by the upregulation of α-smooth muscle actin and collagen synthesis. Additionally, in this process, the loss of the epithelial marker E-cadherin was observed. Furthermore, the expressions of senescence markers, such as p21 and p53, were upregulated upon bleomycin treatment, thereby intensifying the fibrotic condition. Accordingly, the molecular pathway mediating the bleomycin-induced fibrosis was explored in the current study.
Collapse
Affiliation(s)
- Karthika Muthuramalingam
- Department of Biochemistry, School of Medicine, Jeju National University, Jeju, 63243, Republic of Korea
| | - Moonjae Cho
- Department of Biochemistry, School of Medicine, Jeju National University, Jeju, 63243, Republic of Korea.,Institute of Medical Science, Jeju National University, Jeju, 63241, Republic of Korea.,Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, 63241, Republic of Korea
| | - Youngmee Kim
- Department of Biochemistry, School of Medicine, Jeju National University, Jeju, 63243, Republic of Korea
| |
Collapse
|
6
|
Sun JM, Xu HT, Zhao L, Zhang YB, Kang PC, Song ZF, Liu HS, Cui YF. Induction of cell-cycle arrest and apoptosis in human cholangiocarcinoma cells by pristimerin. J Cell Biochem 2019; 120:12002-12009. [PMID: 30825242 DOI: 10.1002/jcb.28485] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 01/24/2023]
Abstract
Pristimerin, a triterpenoid isolated from Celastraceae and Hippocrateaceae, is known to induce cytotoxicity in several cancer cell lines. However, whether pristimerin can induce apoptosis in cholangiocarcinoma cells and the underlying mechanism remain unexplored. We assessed the function of human cholangiocarcinoma QBC and RBE cell lines using various experimental methods such as the cell viability assay to elucidate the viability of cells, flow cytometry to detect the death rate of cells, and Western blot analysis to evaluate the expression of cell cycle-related proteins and autophagy-related proteins. Human cholangiocarcinoma QBC cells were transplanted to nude mice to establish an animal model, and the effect of pristimerin on tumor growth in this model was observed. QBC and RBE cell lines treated with pristimerin (0, 5, 10, and 20 μmol/L) demonstrated the induction of apoptosis in a dose-dependent manner. The cell viability assay revealed a reduction in the cell viability with an increase in the pristimerin concentration. Similarly, flow cytometry revealed a gradual increase in the cell death rate with an increase in the pristimerin concentration. In addition, pristimerin significantly lowered the expression of apoptosis-related proteins (Bcl-2, Bcl-xL, and procaspase-3), but increased the Bax expression. Furthermore, pristimerin resulted in the G0/G1 cell-cycle arrest, reducing the expression of cell cycle-related proteins (cyclin E, CDK2, and CDK4), and increased the expression of autophagy-related proteins (LC3) in QBC cell line. Treatment with pristimerin could inhibit tumor growth in the nude mouse model. Overall, this study suggests the potential effect of pristimerin on the cell-cycle arrest and apoptosis in human cholangiocarcinoma cells.
Collapse
Affiliation(s)
- Jian-Min Sun
- Department of Hepatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Hai-Tao Xu
- Department of Hepatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Liang Zhao
- Department of Hepatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yu-Bao Zhang
- Department of Hepatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Peng-Cheng Kang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zeng-Fu Song
- Department of Hepatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Hai-Shi Liu
- Department of Hepatobiliary Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Yun-Fu Cui
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| |
Collapse
|
7
|
Jensen K, WuWong DJ, Wong S, Matsuyama M, Matsuyama S. Pharmacological inhibition of Bax-induced cell death: Bax-inhibiting peptides and small compounds inhibiting Bax. Exp Biol Med (Maywood) 2019; 244:621-629. [PMID: 30836793 DOI: 10.1177/1535370219833624] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
IMPACT STATEMENT Bax induces mitochondria-dependent programed cell death. While cytotoxic drugs activating Bax have been developed for cancer treatment, clinically effective therapeutics suppressing Bax-induced cell death rescuing essential cells have not been developed. This mini-review will summarize previously reported Bax inhibitors including peptides, small compounds, and antibodies. We will discuss potential applications and the future direction of these Bax inhibitors.
Collapse
Affiliation(s)
- Kelsey Jensen
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - David Jasen WuWong
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Sean Wong
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Mieko Matsuyama
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Shigemi Matsuyama
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| |
Collapse
|
8
|
Malsin ES, Kamp DW. The mitochondria in lung fibrosis: friend or foe? Transl Res 2018; 202:1-23. [PMID: 30036495 DOI: 10.1016/j.trsl.2018.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/24/2018] [Accepted: 05/27/2018] [Indexed: 02/07/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) and other forms of lung fibrosis are age-associated diseases with increased deposition of mesenchymal collagen that promotes respiratory malfunction and eventual death from respiratory failure. Our understanding of the pathobiology underlying pulmonary fibrosis is incomplete and current therapies available to slow or treat lung fibrosis are limited. Evidence reviewed herein demonstrates key involvement of mitochondrial dysfunction in diverse pulmonary cell populations, including alveolar epithelial cells (AEC), fibroblasts, and macrophages and/or immune cells that collectively advances the development of pulmonary fibrosis. The mitochondria have an important role in regulating whether fibrogenic stimuli results in the return of normal healthy function ("friend") or the development of pulmonary fibrosis ("foe"). In particular, we summarize the evidence suggesting that AEC mitochondrial dysfunction is important in mediating lung fibrosis signaling via mechanisms involving imbalances in the levels of reactive oxygen species, endoplasmic reticulum stress response, mitophagy, apoptosis and/or senescence, and inflammatory signaling. Further, we review the emerging evidence suggesting that dysfunctional mitochondria in AECs and other cell types play crucial roles in modulating nearly all aspects of the 9 hallmarks of aging in the context of pulmonary fibrosis as well as some novel molecular pathways that have recently been identified. Finally, we discuss the potential translational aspects of these studies as well as the key knowledge gaps necessary for better informing our understanding of the pathobiology of the mitochondria in mediating pulmonary fibrosis. We reason that targeting deficient mitochondria-derived pathways may provide innovative future treatment strategies that are urgently needed for lung fibrosis.
Collapse
Affiliation(s)
- Elizabeth S Malsin
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, Jesse Brown VA Medical Center and Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David W Kamp
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, Jesse Brown VA Medical Center and Northwestern University Feinberg School of Medicine, Chicago, Illinois.
| |
Collapse
|