1
|
Chen X, Li C, Wang Z, Zhou Y, Chu M. Computational screening of biomarkers and potential drugs for arthrofibrosis based on combination of sequencing and large nature language model. J Orthop Translat 2024; 44:102-113. [PMID: 38304615 PMCID: PMC10831815 DOI: 10.1016/j.jot.2023.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 02/03/2024] Open
Abstract
Background Arthrofibrosis (AF) is a fibrotic joint disease resulting from excessive collagen production and fibrous scar formation after total knee arthroplasty (TKA). This devastating complication may cause consistent pain and dramatically reduction of functionality. Unfortunately, the conservative treatments to prevent the AF in the early stage are largely unknown due to the lack of specific biomarkers and reliable therapeutic targets. Methods In this study, we extracted1782 fibrosis related genes (FRGs) from 373,461published literature based on the large natural language processing models (ChatGPT) and intersected with the 2750 differential expressed genes (DEGs) from mRNA microarray (GSE135854). A total of 311 potential AF biomarker genes (PABGs) were obtained and functional analysis were performed including gene ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Subsequently, we accomplished validation in AF animal models with immobilization of the unilateral knee joints of 16 rabbits for 1-week, 2-weeks, 3-weeks and 4-weeks. Finally, we tested the biomarkers in a retrospective cohort enrolled 35 AF patients and 35 control group patients. Results We identified G-protein-coupled receptor 17 (GPR17) as a reliable therapeutic biomarker for AF diagnosis with higher AUC (0.819) in the ROC curve. A total of 21 potential drugs targeted to GPR17 were screened. Among them, pranlukast and montelukast have achieved therapeutic effect in animal models. In addition, we established an online AF database for data integration (https://chenxi2023.shinyapps.io/afdbv1). Conclusions These results unveiling therapeutic biomarkers for AF diagnosis, and provide potential drugs for clinical treatment. The translational potential of this article Our study demonstrated that GPR17 holds significant promise as a potential biomarker and therapeutic target for arthrofibrosis. Moreover, pranlukast and montelukast targeted to GPR17 that could be instrumental in the treatment of AF.
Collapse
Affiliation(s)
- Xi Chen
- Department of Adult Joint Reconstructive Surgery, Beijing Jishuitan Hospital, Capital Medical University, 31 East Xinjiekou Street, Beijing, 100035, China
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191, China
- NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China
| | - Cheng Li
- Department of Adult Joint Reconstructive Surgery, Beijing Jishuitan Hospital, Capital Medical University, 31 East Xinjiekou Street, Beijing, 100035, China
| | - Ziyuan Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191, China
- NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China
| | - Yixin Zhou
- Department of Adult Joint Reconstructive Surgery, Beijing Jishuitan Hospital, Capital Medical University, 31 East Xinjiekou Street, Beijing, 100035, China
| | - Ming Chu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, 100191, China
- NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China
| |
Collapse
|
2
|
Baicalin Ameliorates Radiation-Induced Lung Injury by Inhibiting the CysLTs/CysLT1 Signaling Pathway. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2765354. [PMID: 35783527 PMCID: PMC9249482 DOI: 10.1155/2022/2765354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/06/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022]
Abstract
Objective Radiation-induced lung injury (RILI) is a common complication of radiotherapy for thoracic tumors. This study investigated the alleviating effect of baicalin (BA) on RILI and its possible mechanism. Methods RILI model was established by chest irradiation (IR) of C57BL/6 mice for 16 weeks. Different concentrations of BA were administered, and dexamethasone (DXM) was used as a positive control. Then, the lung pathological changes were observed by HE and Masson staining. The levels of TGF-β, TNF-α, IL-1β, IL-6, CysLT, LTC4, and LTE4 were measured by ELISA. The CysLT1 expression was detected by qPCR, immunohistochemistry, and western blot. Type II AEC cells were pretreated with LTD-4 to establish the RILI cell model and intervened with different concentrations of BA. Then, the collagen I protein level was measured by ELISA. The CysLT1 and α-SMA expression were detected by qPCR, immunofluorescence, and western blot. Results BA could effectively improve lung histopathological changes and pulmonary fibrosis. In vivo, BA could inhibit the levels of TGF-β, TNF-α, IL-1β, and IL-6 and reduce the levels of CysLT, LTC4, and LTE4. In vitro, different concentrations of LTD4 could reduce the viability of type II AEC cells, which could be reversed by the administration of different concentrations of BA. In addition, BA could reduce CysLT1 mRNA, as well as CysLT1 and α-SMA protein levels in vitro and in vivo. Conclusion BA attenuated lung inflammation and pulmonary fibrosis by inhibiting the CysLTs/CysLT1 pathway, thereby protecting against RILI.
Collapse
|
3
|
Hanmandlu A, Zhu L, Mertens TC, Collum S, Bi W, Xiong F, Wang R, Amirthalingam RT, Ren D, Han L, Jyothula SS, Li W, Zheng WJ, Karmouty-Quintana H. Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis (IPF). Am J Respir Cell Mol Biol 2021; 66:53-63. [PMID: 34370624 DOI: 10.1165/rcmb.2020-0437oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF), a devastating, fibro-proliferative chronic lung disorder, is associated with expansion of fibroblasts/myofibroblasts, which leads to excessive production and deposition of extracellular matrix (ECM). IPF is typically clinically identified as end-stage lung disease, after fibrotic processes are well-established and advanced. Fibroblasts have been shown to be critically important in the development and progression of IPF. We hypothesize that differential chromatin access can drive genetic differences in IPF fibroblasts relative to healthy fibroblasts. To this end, we performed Assay of Transposase-Accessible Chromatin (ATAC)-sequencing to identify differentially accessible regions within the genomes of fibroblasts from healthy and IPF lungs. Multiple motifs were identified to be enriched in IPF fibroblasts compared to healthy fibroblasts, including binding motifs for TWIST1 and FOXA1. RNA-sequencing identified 93 genes that could be annotated to differentially accessible regions. Pathway analysis of the annotated genes identified cellular adhesion, cytoskeletal anchoring, and cell differentiation as important biological processes. In addition, single nucleotide polymorphisms (SNPs) analysis showed that linkage disequilibrium (LD) blocks of IPF risk SNPs with IPF accessible regions that have been identified to be located in genes which are important in IPF, including MUC5B, TERT and TOLLIP. Validation studies in isolated lung tissue confirmed increased expression for TWIST1 and FOXA1 in addition to revealing SHANK2 and CSPR2 as novel targets. Thus, modulation of differential chromatin access may be an important mechanism in the pathogenesis of lung fibrosis.
Collapse
Affiliation(s)
- Ankit Hanmandlu
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Lisha Zhu
- University of Texas Health Science Center at Houston, 12340, School of Biomedical Informatics, Houston, Texas, United States
| | - Tinne Cj Mertens
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Scott Collum
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Weizhen Bi
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Feng Xiong
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Ruoyu Wang
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | | | - Dewei Ren
- Houston Methodist Hospital, 23534, J.C. Walter Jr. Transplant Center, Houston, Texas, United States
| | - Leng Han
- The University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - Soma Sk Jyothula
- University of Texas Health Science Center at Houston, 12340, Internal Medicine, Houston, Texas, United States
| | - Wenbo Li
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States
| | - W Jim Zheng
- The University of Texas Health Science Center at Houston, 12340, School of Biomedical Informatics, Houston, Texas, United States
| | - Harry Karmouty-Quintana
- University of Texas Health Science Center at Houston, 12340, Biochemistry and Molecular Biology, Houston, Texas, United States;
| |
Collapse
|
4
|
Kowal-Bielecka O, Chwiesko-Minarowska S, Bernatowicz PL, Allanore Y, Radstake T, Matucci-Cerinic M, Broen J, Hesselstrand R, Krasowska D, Riemekasten G, Vonk M, Kowalczuk O, Bielecki M, Milewski R, Chyczewski L, Niklinski J, Kowal K. The arachidonate 5-lipoxygenase activating protein gene polymorphism is associated with the risk of scleroderma-related interstitial lung disease: a multicentre European Scleroderma Trials and Research group (EUSTAR) study. Rheumatology (Oxford) 2017; 56:844-852. [DOI: 10.1093/rheumatology/kew499] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Indexed: 01/02/2023] Open
|
5
|
Kurai J, Watanabe M, Sano H, Hantan D, Tohda Y, Shimizu E. Effects of Asian Dust Particles on the Early-Stage Antigen-Induced Immune Response of Asthma in NC/Nga Mice. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:E1144. [PMID: 27854355 PMCID: PMC5129354 DOI: 10.3390/ijerph13111144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/03/2016] [Accepted: 11/14/2016] [Indexed: 12/15/2022]
Abstract
Asian dust (AD) can aggravate airway inflammation in asthma, but the association between AD and the development of asthma remains unclear. This study aimed to investigate the effects of AD on the early stage of antigen sensitization using a mouse model of asthma, as well as the role of leukotrienes (LTs) in antigen-induced airway inflammation potentiated by AD particles. NC/Nga mice were co-sensitized by intranasal instillation of AD particles and/or Dermatophagoides farinae (Df) for five consecutive days. Df-sensitized mice were stimulated with an intranasal Df challenge at seven days. Mice were treated with the type 1 cysteinyl LT (CysLT₁) receptor antagonist orally 4 h before and 1 h after the allergen challenge. At 24 h post-challenge, the differential leukocyte count, inflammatory cytokines, and LTs in bronchoalveolar lavage fluid were assessed, and airway inflammation was evaluated histopathologically. AD augmented neutrophilic and eosinophilic airway inflammation with increased CysLTs and dihydroxy-LT in a mouse model of asthma. The CysLT₁ receptor antagonist was shown to attenuate both neutrophilic and eosinophilic airway inflammation augmented by AD. Therefore, exposure to AD may be associated with the development of asthma and LTs may play important roles in airway inflammation augmented by AD.
Collapse
Affiliation(s)
- Jun Kurai
- Department of Respiratory Medicine and Rheumatology, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago 683-8504, Japan.
| | - Masanari Watanabe
- Department of Respiratory Medicine and Rheumatology, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago 683-8504, Japan.
| | - Hiroyuki Sano
- Department of Respiratory Medicine and Allergology, Kinki University, 377-2 Ohnohigashi, Osakasayama 589-0014, Japan.
| | - Degejirihu Hantan
- Department of Respiratory Medicine and Rheumatology, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago 683-8504, Japan.
| | - Yuji Tohda
- Department of Respiratory Medicine and Allergology, Kinki University, 377-2 Ohnohigashi, Osakasayama 589-0014, Japan.
| | - Eiji Shimizu
- Department of Respiratory Medicine and Rheumatology, Faculty of Medicine, Tottori University, 36-1 Nishi-cho, Yonago 683-8504, Japan.
| |
Collapse
|
6
|
Uncoupling between inflammatory and fibrotic responses to silica: evidence from MyD88 knockout mice. PLoS One 2014; 9:e99383. [PMID: 25050810 PMCID: PMC4106757 DOI: 10.1371/journal.pone.0099383] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 05/14/2014] [Indexed: 12/21/2022] Open
Abstract
The exact implication of innate immunity in granuloma formation and irreversible lung fibrosis remains to be determined. In this study, we examined the lung inflammatory and fibrotic responses to silica in MyD88-knockout (KO) mice. In comparison to wild-type (WT) mice, we found that MyD88-KO animals developed attenuated lung inflammation, neutrophil accumulation and IL-1β release in response to silica. Granuloma formation was also less pronounced in MyD88-KO mice after silica. This limited inflammatory response was not accompanied by a concomitant attenuation of lung collagen accumulation after silica. Histological analyses revealed that while pulmonary fibrosis was localized in granulomas in WT animals, it was diffusely distributed throughout the parenchyma in MyD88-KO mice. Robust collagen accumulation was also observed in mice KO for several other components of innate immunity (IL-1R, IL-1, ASC, NALP3, IL-18R, IL-33R, TRIF, and TLR2-3-4,). We additionally show that pulmonary fibrosis in MyD88-KO mice was associated with the accumulation of pro-fibrotic regulatory T lymphocytes (T regs) and pro-fibrotic cytokine expression (TGF-β, IL-10 and PDGF-B), not with T helper (Th) 17 cell influx. Our findings indicate that the activation of MyD88-related innate immunity is central in the establishment of particle-induced lung inflammatory and granuloma responses. The development of lung fibrosis appears uncoupled from inflammation and may be orchestrated by a T reg-associated pathway.
Collapse
|
7
|
Cysteinyl leukotriene receptor-1 antagonists as modulators of innate immune cell function. J Immunol Res 2014; 2014:608930. [PMID: 24971371 PMCID: PMC4058211 DOI: 10.1155/2014/608930] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 12/20/2022] Open
Abstract
Cysteinyl leukotrienes (cysLTs) are produced predominantly by cells of the innate immune system, especially basophils, eosinophils, mast cells, and monocytes/macrophages. Notwithstanding potent bronchoconstrictor activity, cysLTs are also proinflammatory consequent to their autocrine and paracrine interactions with G-protein-coupled receptors expressed not only on the aforementioned cell types, but also on Th2 lymphocytes, as well as structural cells, and to a lesser extent neutrophils and CD8+ cells. Recognition of the involvement of cysLTs in the immunopathogenesis of various types of acute and chronic inflammatory disorders, especially bronchial asthma, prompted the development of selective cysLT receptor-1 (cysLTR1) antagonists, specifically montelukast, pranlukast, and zafirlukast. More recently these agents have also been reported to possess secondary anti-inflammatory activities, distinct from cysLTR1 antagonism, which appear to be particularly effective in targeting neutrophils and monocytes/macrophages. Underlying mechanisms include interference with cyclic nucleotide phosphodiesterases, 5′-lipoxygenase, and the proinflammatory transcription factor, nuclear factor kappa B. These and other secondary anti-inflammatory mechanisms of the commonly used cysLTR1 antagonists are the major focus of the current review, which also includes a comparison of the anti-inflammatory effects of montelukast, pranlukast, and zafirlukast on human neutrophils in vitro, as well as an overview of both the current clinical applications of these agents and potential future applications based on preclinical and early clinical studies.
Collapse
|
8
|
Mossman BT, Glenn RE. Bioreactivity of the crystalline silica polymorphs, quartz and cristobalite, and implications for occupational exposure limits (OELs). Crit Rev Toxicol 2013; 43:632-60. [PMID: 23863112 DOI: 10.3109/10408444.2013.818617] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Silica or silicon dioxides (SiO₂) are naturally occurring substances that comprise the vast majority of the earth's crust. Because of their prevalence and commercial applications, they have been widely studied for their potential to induce pulmonary fibrosis and other disorders. Historically, the focus in the workplace has been on the development of inflammation and fibrotic lung disease, the basis for promulgating workplace standards to protect workers. Crystalline silica (CS) polymorphs, predominantly quartz and cristobalite, are used in industry but are different in their mineralogy, chemistry, surface features, size dimensions and association with other elements naturally and during industrial applications. Epidemiologic, clinical and experimental studies in the literature historically have predominantly focused on quartz polymorphs. Thus, in this review, we summarize past scientific evaluations and recent peer-reviewed literature with an emphasis on cristobalite, in an attempt to determine whether quartz and cristobalite polymorphs differ in their health effects, toxicity and other properties that may dictate the need for various standards of protection in the workplace. In addition to current epidemiological and clinical reports, we review in vivo studies in rodents as well as cell culture studies that shed light on mechanisms intrinsic to the toxicity, altered cell responses and protective or defense mechanisms in response to these minerals. The medical and scientific literature indicates that the mechanisms of injury and potential causation of inflammation and fibrotic lung disease are similar for quartz and cristobalite. Our analysis of these data suggests similar occupational exposure limits (OELs) for these minerals in the workplace.
Collapse
Affiliation(s)
- Brooke T Mossman
- Department of Pathology, University of Vermont College of Medicine, Burlington, VT 05405-0068, USA.
| | | |
Collapse
|
9
|
Brass DM, Spencer JC, Li Z, Potts-Kant E, Reilly SM, Dunkel MK, Latoche JD, Auten RL, Hollingsworth JW, Fattman CL. Innate immune activation by inhaled lipopolysaccharide, independent of oxidative stress, exacerbates silica-induced pulmonary fibrosis in mice. PLoS One 2012; 7:e40789. [PMID: 22815821 PMCID: PMC3397936 DOI: 10.1371/journal.pone.0040789] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/13/2012] [Indexed: 12/03/2022] Open
Abstract
Acute exacerbations of pulmonary fibrosis are characterized by rapid decrements in lung function. Environmental factors that may contribute to acute exacerbations remain poorly understood. We have previously demonstrated that exposure to inhaled lipopolysaccharide (LPS) induces expression of genes associated with fibrosis. To address whether exposure to LPS could exacerbate fibrosis, we exposed male C57BL/6 mice to crystalline silica, or vehicle, followed 28 days later by LPS or saline inhalation. We observed that mice receiving both silica and LPS had significantly more total inflammatory cells, more whole lung lavage MCP-1, MIP-2, KC and IL-1β, more evidence of oxidative stress and more total lung hydroxyproline than mice receiving either LPS alone, or silica alone. Blocking oxidative stress with N-acetylcysteine attenuated whole lung inflammation but had no effect on total lung hydroxyproline. These observations suggest that exposure to innate immune stimuli, such as LPS in the environment, may exacerbate stable pulmonary fibrosis via mechanisms that are independent of inflammation and oxidative stress.
Collapse
Affiliation(s)
- David M Brass
- Neonatology Division, Department of Pediatrics, Neonatal Perinatal Research Institute, Duke University Medical Center, Durham, North Carolina, United States of America.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Fireman E. A silica-induced pulmonary fibrosis model: are we closer to 'real life'? Int Arch Allergy Immunol 2012; 158:211-2. [PMID: 22378025 DOI: 10.1159/000335237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|