Genomics of Chronic Obstructive Pulmonary Disease (COPD); Exploring the SNPs of Protease-Antiprotease Pathway

The genomic landscape of chronic obstructive pulmonary disease: Insights from nutrigenomics

Chronic obstructivе pulmonary disеasе (COPD), a rеspiratory disеasе, is influenced by a combination of gеnеtic and еnvironmеntal factors. Thе fiеld of nutrigеnomics, which studiеs thе intеrplay bеtwееn diеt and gеnеs, provides valuable insights into thе gеnomic landscapе of COPD and its implications for production and managеmеnt. This rеviеw providеs a comprеhеnsivе ovеrviеw of thе gеnеtic aspеcts of COPD and thе rolе of nutrigеnomics in advancing our undеrstanding of thе undеrlying mеchanisms. Through studies of gеnomе-widе associations, researchers have identified gеnеtic factors that contribute to suscеptibility to COPD. Thеsе gеnеs arе associatеd with oxidativе strеss, inflammation, and antioxidant dеfеnsе mеchanisms. Nutrigеnomics rеsеarch is currеntly invеstigating how diеtary componеnts interact with gеnеtic variations to modulatе thе dеvеlopmеnt of COPD. Antioxidants, omеga-3 fatty acids and vitamin D havе dеmonstratеd potеntial bеnеfits in rеducing inflammation, improving lung function, and minimizing еxacеrbations in patients with COPD. Therefore, there are sеvеral challеngеs that must be added to the nutrigеnomic rеsеarch. The challenges include thе nееd for largеr clinical trials, adding hеtеrogеnеity and validating biomarkеrs. In the tеrms of futurе dirеctions, prеcision nutrition, gеnе-basеd thеrapiеs, biomarkеr dеvеlopmеnt, intеgration of multi-omics data, systеms biology analysis, longitudinal studiеs, and public hеalth implications arе important arеas to еxplorе. Pеrsonalizеd nutritional intеrvеntions based on an individual's gеnеtic profilе hold grеat promisе for optimizing COPD managеmеnt. In conclusion, nutrigеnomics provides valuable insights into the gеnomic landscapе of COPD and its intеraction with the disease. This knowlеdgе can guidе thе dеvеlopmеnt of pеrsonalizеd diеtary stratеgiеs and gеnе-basеd thеrapiеs for thе prеvеntion and managеmеnt of COPD. Howеvеr, morе rеsеarch is nееdеd to validatе thеsе findings, dеvеlop еffеctivе intеrvеntions, and implеmеnt thеm еffеctivеly in clinical practicе to improvе thе quality of lifе for pеoplе with COPD.

Matrix Metalloproteinases in Chronic Obstructive Pulmonary Disease

Matrix metalloproteinases (MMPs) are proteolytic enzymes that degrade proteins of the extracellular matrix and the basement membrane. Thus, these enzymes regulate airway remodeling, which is a major pathological feature of chronic obstructive pulmonary disease (COPD). Furthermore, proteolytic destruction in the lungs may lead to loss of elastin and the development of emphysema, which is associated with poor lung function in COPD patients. In this literature review, we describe and appraise evidence from the recent literature regarding the role of different MMPs in COPD, as well as how their activity is regulated by specific tissue inhibitors. Considering the importance of MMPs in COPD pathogenesis, we also discuss MMPs as potential targets for therapeutic intervention in COPD and present evidence from recent clinical trials in this regard.

Novel Insights into the Therapeutic Potential of Lung-Targeted Gene Transfer in the Most Common Respiratory Diseases

Over the past decades, a better understanding of the genetic and molecular alterations underlying several respiratory diseases has encouraged the development of new therapeutic strategies. Gene therapy offers new therapeutic alternatives for inherited and acquired diseases by delivering exogenous genetic materials into cells or tissues to restore physiological protein expression and/or activity. In this review, we review (1) different types of viral and non-viral vectors as well as gene-editing techniques; and (2) the application of gene therapy for the treatment of respiratory diseases and disorders, including pulmonary arterial hypertension, idiopathic pulmonary fibrosis, cystic fibrosis, asthma, alpha-1 antitrypsin deficiency, chronic obstructive pulmonary disease, non-small-cell lung cancer, and COVID-19. Further, we also provide specific examples of lung-targeted therapies and discuss the major limitations of gene therapy.

Genetic Polymorphism of Matrix Metalloproteinase 9 and Susceptibility to Chronic Obstructive Pulmonary Disease: A Meta-analysis

Background

To systematically analyze the influence of genetic polymorphisms of matrix metalloproteinase 9 (MMP9) on susceptibility to chronic obstructive pulmonary disease (COPD).

Methods

Relevant literatures reporting MMP9 and susceptibility to COPD in PubMed, Web of Science, VIP, Wanfang and CNKI databases were searched using the key words "matrix metalloproteinases 9/MMP9, COPD/chronic obstructive pulmonary disease". Data of eligible literatures were extracted and analyzed for the odds ratio (OR) and corresponding 95% CI.

Results

A total of 16 independent studies reporting MMP9-1562C/T and COPD patients were enrolled and analyzed. None of the genetic models revealed the relationship between MMP9-1562C/T and susceptibility to COPD. Subgroup analyses identified lower risk of COPD in Chinese population carrying the TT genotype for theMMP9 rs3918242 relative to those carrying CT and CC genotypes (P=0.03, OR=0.67, 95% CI=0.46-0.97).

Conclusions

Chinese population carrying the TT genotype for the MMP-9 rs3918242 present lower susceptibility to COPD relative to those carrying CT and CC genotypes.

New Insights into the Role of NLRP3 Inflammasome in Pathogenesis and Treatment of Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disease characterized by chronic airway obstruction and emphysema. Accumulating studies have shown that the onset and development of COPD are related to an aberrant immune response induced by the dysregulation of a number of genetic and environmental factors, while the exact pathogenesis of this disease is not well defined. Emerging studies based on tests on samples from COPD patients, animal models, pharmacological and genetic data suggest that the NLR family pyrin domain containing 3 (NLRP3) inflammasome activation is required in the lung inflammatory responses in the development of COPD. Although the available clinical studies targeting the inflammasome effector cytokine, IL-1β, or IL-1 signaling do not show positive outcomes for COPD treatment, many alternative strategies have been proposed by recent emerging studies. Here, we highlight the recent progress in our understanding of the role of the NLRP3 inflammasome in COPD and propose possible future studies that may further elucidate the roles of the inflammasome in the pathogenesis or the intervention of this inflammatory lung disease.

The rat model of COPD skeletal muscle dysfunction induced by progressive cigarette smoke exposure: a pilot study

Background

Chronic obstructive pulmonary disease (COPD) skeletal muscle dysfunction is a prevalent malady that significantly affects patients’ prognosis and quality of life. Although the study of this disease has attracted considerable attention, a definite animal model is yet to be established. This study investigates whether smoke exposure could lead to the development of a COPD skeletal muscle dysfunction model in rats.

Methods

Sprague Dawley rats were randomly divided into model (MG, n = 8) and control groups (CG, n = 6). The MG was exposed to cigarette smoke for 16 weeks while the CG was not. The body weight and forelimb grip strength of rats were monitored monthly. The pulmonary function and the strength of tibialis anterior muscle were assessed in vitro and compared after establishing the model. The histological changes in lung and gastrocnemius muscles were observed. The expressions of interleukin (IL)-6, IL-8, and tumor necrosis factor (TNF)-α were detected by ELISA, while the expressions of Atrogin-1 and MuRF1 in the gastrocnemius muscle were determined by Western blotting.

Results

Smoke exposure slowly increases the body weight and forelimb grip strength of MG rats, compared to CG rats. However, it significantly decreases the pulmonary ventilation function and the skeletal muscle contractility of the MG in vitro. Histologically, the lung tissues of MG show typical pathological manifestations of emphysema, while the skeletal muscles present muscular atrophy. The expressions of IL-6, IL-8, and TNF-α in MG rats are significantly higher than those measured in CG rats. Increased levels of Atrogin-1 and MuRF1 were also detected in the gastrocnemius muscle tissue of MG.

Conclusion

Progressive smoking exposure decreases the contractile function of skeletal muscles, leading to muscular atrophy. It also increases the expressions of inflammatory and muscle protein degradation factors in COPD rats. This indicates that smoke exposure could be used to establish a COPD skeletal muscle dysfunction model in rats.

The correlation of age and body mass index with the level of both protease MMP3 and anti-protease TIMP-1 among Indonesian patients with chronic obstructive pulmonary disease: a preliminary findings

Objectives

Individuals with chronic obstructive pulmonary disease (COPD) are usually > 50 years of age and have a low body mass index (BMI). An imbalance between matrix metalloproteinases (MMPs), including MMP-3, and tissue inhibitor of metalloproteinase 1 (TIMP-1), play a role in tissue degradation of lung extracellular matrix among COPD individuals. The purpose of the present study was to correlate age and/or BMI with salivary levels of MMP-3 and TIMP-1 among Indonesian subjects with COPD.

Results

Thirty COPD patients were recruited to undergo thorough physical assessment and saliva collection for evaluating TIMP-1 and MMP-3 levels using commercially available kits enzyme-linked immunosorbent assay method. The mean (standard deviation) participant age and BMI were 60.5 (8.13) years, and 23.1 (4.75) kg/m², respectively. Furthermore, the mean (standard deviation) of TIMP-1 and MMP3 levels were 23.99 (6.85) ng/mL and 1.81 (1.167) μM, respectively. Age was negatively correlated with MMP-3 (P < 0.05), but not with TIMP-1 levels. Age and BMI were not correlated with TIMP-1 level (P > 0.05). Collectively, this study demonstrated that age has a negative correlation with the protease marker (i.e. MMP-3), but not the anti-protease marker (TIMP-1). BMI was not correlated with either protease/anti-protease marker among Indonesian subjects with COPD.

Integrating Transcriptomics, Proteomics, and Metabolomics Profiling with System Pharmacology for the Delineation of Long-Term Therapeutic Mechanisms of Bufei Jianpi Formula in Treating COPD

In previous work, we identified 145 active compounds from Bufei Jianpi formula (BJF) by system pharmacology and found that BJF showed short-term effect on chronic obstructive pulmonary disease (COPD) rats. Here, we applied the transcriptomic, proteomic, and metabolomics approaches to illustrate the long-term anti-COPD action and its system mechanism of BJF. BJF has obvious anti-COPD effect through decreasing inflammatory cytokines level, preventing protease-antiprotease imbalance and collagen deposition on week 32 by continuous oral administration to rats from weeks 9 to 20. Subsequently, applying the transcriptomic, proteomic, and metabolomics techniques, we detected a number of regulated genes, proteins, and metabolites, mainly related to antioxidant activity, focal adhesion, or lipid metabolism, in lung tissues of COPD and BJF-treated rats. Afterwards, we integrated system pharmacology target, transcript, protein, and metabolite data sets and found that many genes, proteins, and metabolites in rats BJF-treated group and the target proteins of BJF were mainly attributed to lipid metabolism, inflammatory response, oxidative stress, and focal adhesion. Taken together, BJF displays long-term anti-COPD effect probably by system regulation of the lipid metabolism, inflammatory response pathways oxidative stress, and focal adhesion.

Role of Proteases in Lung Disease: A Brief Overview

Proteases play an important role in health and disease of the lung. In the normal lungs, proteases maintain their homeostatic functions that regulate processes like its regeneration and repair. Dysregulation of proteases–antiproteases balance is crucial in the manifestation of different types of lung diseases. Chronic inflammatory lung pathologies are associated with a marked increase in protease activities. Thus, in addition to protease activities, inhibition of anti-proteolytic control mechanisms are also important for effective microbial infection and inflammation in the lung. Herein, we briefly summarize the role of different proteases and to some extent antiproteases in regulating a variety of lung diseases.

Genetic polymorphisms of matrix metalloproteinases and protein levels in chronic obstructive pulmonary disease in a Mexican population

AIM

To evaluate association of single nucleotide polymorphisms (SNPs) in the MMP1, MMP2, MMP9 and MMP12 genes and serum MMP-2 and MMP-9 levels in smoking chronic obstructive pulmonary disease (COPD) patients.

MATERIALS & METHODS

Genotyping using real-time PCR in 330 smokers with COPD (COPD), 658 smokers without COPD (SNC) and 150 nonsmokers (NCNS), the analysis of samples used was χ(2) test. Using ELISA, the proteins were evaluated. Multiple comparisons were made by ANOVA.

RESULTS

rs243864 (OR: 7.44; 95% CI: 3.62-15.26) and rs11646643 (OR: 1.58; 95% CI: 1.07-2.34) of the MMP-2 gene and rs3918253 (OR: 1.72; 95% CI: 1.08-2.71) of the MMP-9 gene, were associated with the risk of COPD. Serum MMP-2 level in the COPD group was lower compared with SNC (p < 0.05). Serum MMP-9 level was elevated in the COPD group compared with SNC (p < 0.05).

CONCLUSION

Polymorphisms in MMP2 and MMP9 but not in MMP1 and MMP12 are associated with the risk of COPD in the Mexican mestizo population.

Particulate matter (PM₁₀) induces metalloprotease activity and invasion in airway epithelial cells

Airborne particulate matter with an aerodynamic diameter ≤ 10 μm (PM10) is a risk factor for the development of lung diseases and cancer. The aim of this work was to identify alterations in airway epithelial (A549) cells induced by PM10 that could explain how subtoxic exposure (10 μg/cm(2)) promotes a more aggressive in vitro phenotype. Our results showed that cells exposed to PM10 from an industrial zone (IZ) and an urban commercial zone (CZ) induced an increase in protease activity and invasiveness; however, the cell mechanism is different, as only PM10 from CZ up-regulated the activity of metalloproteases MMP-2 and MMP-9 and disrupted E-cadherin/β-catenin expression after 48 h of exposure. These in vitro findings are relevant in terms of the mechanism action of PM10 in lung epithelial cells, which could be helpful in understanding the pathogenesis of some human illness associated with highly polluted cities.

CCN1 secretion and cleavage regulate the lung epithelial cell functions after cigarette smoke

Despite extensive research, the pathogenesis of cigarette smoking (CS)-associated emphysema remains incompletely understood, thereby impeding development of novel therapeutics, diagnostics, and biomarkers. Here, we report a novel paradigm potentially involved in the development of epithelial death and tissue loss in CS-associated emphysema. After prolonged exposure of CS, CCN1 cleavage was detected both in vitro and in vivo. Full-length CCN1 (flCCN1) was secreted in an exosome-shuttled manner, and secreted plasmin converted flCCN1 to cleaved CCN1 (cCCN1) in extracellular matrix. Interestingly, exosome-shuttled flCCN1 facilitated the interleukin (IL)-8 and vascular endothelial growth factor (VEGF) release in response to cigarette smoke extract (CSE). Therefore, flCCN1 potentially promoted CS-induced inflammation via IL-8-mediated neutrophil recruitment and also maintained the lung homeostasis via VEGF secretion. Interestingly, cCCN1 abolished these functions. Furthermore, cCCN1 promoted protease and matrix metalloproteinase (MMP)-1 production after CSE. These effects were mainly mediated by the COOH-terminal fragments of CCN1 after cleavage. Both the decrease of VEGF and the elevation of MMPs favor the development of emphysema. cCCN1, therefore, likely contributes to the epithelial cell damage after CS. Additionally, CSE and cCCN1 both stimulated integrin-α7 expressions in lung epithelial cells. The integrin-α7 appeared to be the binding receptors of cCCN1 and, subsequently, mediated its cellular function by promoting MMP1. Consistent with our observation on the functional roles of cCCN1 in vitro, elevated cCCN1 level was found in the bronchoalveolar lavage fluid from mice with emphysematous changes after 6 mo CS exposure. Taken together, we hypothesize that cCCN1 promoted the epithelial cell death and tissue loss after prolonged CS exposure.