Analysis of differentially expressed genes and signaling pathways involved in atherosclerosis and chronic obstructive pulmonary disease

Lipid metabolism reprogramming in chronic obstructive pulmonary disease

Chronic Obstructive Pulmonary Disease (COPD) is a complex and diverse respiratory disorder, characterized by ongoing respiratory symptoms and restricted airflow. The major clinical manifestations typically encompass chronic cough, sputum production, and wheezing. The main pathological characteristics involve infiltration of inflammatory cells, overproduction of mucus, and damage to the alveolar walls. The underlying causes of COPD are complex and remain incompletely elucidated, thought to originate from the combined effect of various factors. Lipids, as hydrophobic molecules, fulfill three fundamental functions: energy storage, membrane biosynthesis, and signal transduction. Lipid metabolism is intricately intertwined with various metabolic pathways and plays a pivotal role in the complex pathogenesis of COPD. Delving into lipid metabolism, as well as the particular modifications and roles of lipid molecules in cells, is of paramount importance in the context of COPD. This review primarily aims to elucidate the role of fatty acid metabolism in the onset and progression of COPD. Additionally, it examines the potential of lipid metabolism reprogramming as a promising therapeutic approach, illuminating new paths for the management and treatment of this disabling respiratory condition.

The Role of Inflammation in the Pathogenesis of Comorbidity of Chronic Obstructive Pulmonary Disease and Pulmonary Tuberculosis

The comorbid course of chronic obstructive pulmonary disease (COPD) and pulmonary tuberculosis is an important medical and social problem. Both diseases, although having different etiologies, have many overlapping relationships that mutually influence their course and prognosis. The aim of the current review is to discuss the role of different immune mechanisms underlying inflammation in COPD and pulmonary tuberculosis. These mechanisms are known to involve both the innate and adaptive immune system, including various cellular and intercellular interactions. There is growing evidence that immune mechanisms involved in the pathogenesis of both COPD and tuberculosis may jointly contribute to the tuberculosis-associated obstructive pulmonary disease (TOPD) phenotype. Several studies have reported prior tuberculosis as a risk factor for COPD. Therefore, the study of the mechanisms that link COPD and tuberculosis is of considerable clinical interest.

In silico exploration of phytochemicals as inhibitors for acute myeloid leukemia by targeting LIN28A gene: A cheminformatics study

BACKGROUND

Recent discoveries have illustrated that Lin28A is an oncogene in various cancers, particularly acute myeloid leukemia (AML). The upregulation of Lin28A can actively contribute to tumorigenesis and migration processes in multiple organs. Hence, the inhibition of Lin28A can be achieved by applying phytochemical herbals and targeting Lin28A protein using a computer-aided drug design (CAAD) approach.

METHODS

In this study, we comprehensively applied several bioinformatics tools, including gene ontologies, gene enrichment analysis, and protein-protein interactions (PPI), to determine the biological pathways, functional gene ontology, and biological pathway. Furthermore, we investigated a list of phytochemical herbs as a candidate drug by applying a computation technique involving molecular docking, density functional theory (DFT), molecular dynamics simulation (MDs), and pharmacokinetic and physiochemical properties by applying the SwissADME, pkCSM, and Molsoft LLC web-servers.

RESULTS

The Lin28A gene is related to two significant enrichment pathways, including proteoglycans in cancer and the pluripotency of stem cells through interactions with different genes such as MAPK12, MYC, MTOR, and PIK3CA. Interestingly, limonin, 18β Glycyrrhetic Acid, and baicalein have the highest binding energy scores of -8.4, -8.2, and -7.3 kcal/mol, respectively. The DFT study revealed that baicalein has a higher reactivity than limonin and 18β-Glycyrrhetic due to a small energy gap between LUMO and HUMO. Molecular dynamics simulation exhibited that baicalein complex with Lin28A protein is more stable than other complexes during simulation time due to low fluctuation with simulation periods as compared with other complexes, which indicated that baicalein was more fitting to docking and combining in the protein cave because of the largest number of H-bonds available for the docking simulation process. Furthermore, the drug-likeness and ADMET profiles revealed the activity of limonin, baicalein, and 18β-glycyrrhizic Acid, which possess significant inhibiting Lin28A proteins.

CONCLUSION

This study elucidated that baicalein, 18β-glycyrrhizic, and limonin may be applied as potential candidates for targeting Lin28A as an active oncogene for acute myeloid leukemia.

Engineered Bimetallic MOF-Crafted Bullet Aids in Penetrating Serum Metabolic Traits of Chronic Obstructive Pulmonary Disease

Metabolomics analysis based on body fluids, combined with high-throughput laser desorption and ionization mass spectrometry (LDI-MS), holds great potential and promising prospects for disease diagnosis and screening. On the other hand, chronic obstructive pulmonary disease (COPD) currently lacks innovative and powerful diagnostic and screening methods. In this work, CoFeNMOF-D, a metal-organic framework (MOF)-derived metal oxide nanomaterial, was synthesized and utilized as a matrix to assist LDI-MS for extracting serum metabolic fingerprints of COPD patients and healthy controls (HC). Through machine learning algorithms, successful discrimination between the COPD and HC was achieved. Furthermore, four potential biomarkers significantly downregulated in COPD were screened out. The disease diagnostic models based on the biomarkers demonstrated excellent diagnostic performance across different algorithms, with area under the curve (AUC) values reaching 0.931 and 0.978 in the training and validation sets, respectively. Finally, the potential metabolic pathways and disease mechanisms associated with the identified markers were explored. This work advances the application of LDI-based molecular diagnostics in clinical settings.

Early Detection of Atrial Fibrillation in Chronic Obstructive Pulmonary Disease Patients

Atrial fibrillation (AF) is an important medical problem, as it significantly affects patients' quality of life and prognosis. AF often complicates the course of chronic obstructive pulmonary disease (COPD), a widespread disease with heavy economic and social burdens. A growing body of evidence suggests multiple links between COPD and AF. This review considers the common pathogenetic mechanisms (chronic hypoxia, persistent inflammation, endothelial dysfunction, and myocardial remodeling) of these diseases and describes the main risk factors for the development of AF in patients with COPD. The most effective models based on clinical, laboratory, and functional indices are also described, which enable the identification of patients suffering from COPD with a high risk of AF development. Thus, AF in COPD patients is a frequent problem, and the search for new tools to identify patients at a high risk of AF among COPD patients remains an urgent medical problem.

Ultrasonic AccV: a potential indicator of peripheral arteriosclerosis in patients with chronic obstructive pulmonary disease

OBJECTIVE

This study aimed to investigate the risk factors for peripheral arteriosclerosis (PAS) and peripheral artery disease (PAD) in chronic obstructive pulmonary disease (COPD) patients and potential ultrasound indicators that could be used to improve detection.

METHOD

Outpatients seeking care between January 1, 2017, and December 31, 2020, in The First Affiliated Hospital of China Medical University were prospectively recruited. Subjects were divided into COPD and non-COPD (control) groups, and the COPD group was further divided into PAD and non-PAD subgroup, at the same time, PAS and non-PAS subgroup. Indicators of PAD -ankle-brachial index (ABI), indicators of PAS- pulse wave velocity (PWV), and ultrasound indices -peak systolic blood flow velocity (PSV) and blood flow acceleration velocity (AccV) were compared.

RESULT

Sixty-nine (61.6%) of 112 enrolled subjects had COPD. COPD patients had higher age, and blood pressure (BP)lower than controls. Seventeen (24.6%) COPD patients had PAD, the prevalence of PAD increases with the decrease of lung function, and seven (16.3%) non-COPD patients had PAD, however, there was no significant statistical difference between COPD and non-COPD groups. Fifty (72.5%) COPD patients had PAS, and thirty-four (79.1%) non-COPD patients had PAS, however, there was also no significant difference. The PAS subgroup had higher age, body mass index(BMI), body fat percentage(BFP), lower FEV1 and FEV1/FVC, as well as higher levels of right brachial artery and left dorsalis pedis artery AccV. Factors that correlated with ABI were 6MWD, post-bronchodilator FEV1, FEV1/ FVC, and maximal middle expiratory flow between 75% and 25% of FVC. Age, BP, and 6MWD, but not pulmonary function, were associated with brachial-ankle PWV (baPWV). There was a positive correlation between baPWV and radial artery AccV bilaterally.

CONCLUSION

Radial artery AccV correlated well with baPWV, which suggests that ultrasound could be used to assess both morphological and functional changes in vessels, may serving as a better method to identify PAS in high-risk COPD patients.

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.

Identification of Important Genes Associated with the Development of Atherosclerosis

Atherosclerosis is one of the most important medical problems due to its prevalence and significant contribution to the structure of temporary and permanent disability and mortality. Atherosclerosis is a complex chain of events occurring in the vascular wall over many years. Disorders of lipid metabolism, inflammation, and impaired hemodynamics are important mechanisms of atherogenesis. A growing body of evidence strengthens the understanding of the role of genetic and epigenetic factors in individual predisposition and development of atherosclerosis and its clinical outcomes. In addition, hemodynamic changes, lipid metabolism abnormalities, and inflammation are closely related and have many overlapping links in regulation. A better study of these mechanisms may improve the quality of diagnosis and management of such patients.

α-Lipoic acid - a promising agent for attenuating inflammation and preventing steatohepatitis in rats fed a high-fat diet

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a prevalent liver disorder affecting a significant part of the global population. This study aimed to investigate the potential therapeutic effects of α-lipoic acid (α-LA) on the inflammatory response during simple steatosis development and progression into steatohepatitis. The study used the MASLD model in male Wistar rats that were fed a standard diet or a high-fat diet (HFD) for 8 weeks. Throughout the entire experiment, half of the animals received α-LA supplementation. The hepatic activity of pro-inflammatory n-6 and anti-inflammatory n-3 polyunsaturated fatty acid (PUFA) pathways and the concentration of arachidonic acid (AA) in selected lipid fractions were determined by the gas-liquid chromatography (GLC). The hepatic expression of proteins from inflammatory pathway was measured by the Western blot technique. The level of eicosanoids, cytokines and chemokines was assessed by the ELISA or multiplex assay kits. The results showed that α-LA supplementation attenuated the activity of n-6 PUFA pathway in FFA and DAG and increased the activity of n-3 PUFA pathway in PL, TAG and DAG. In addition, the administration of α-LA decreased the concentration of AA in DAG and FFA, indicating its potential protective effect on the deterioration of simple hepatic steatosis. The supplementation of α-LA also increased the expression of COX-1 and COX-2 with the lack of significant changes in prostaglandins profile. We observed an increase in the expression of 12/15-LOX, which was reflected in an increase in lipoxin A4 (LXA4) level. A decrease in pro-inflammatory cytokines and an increase in anti-inflammatory cytokines was also noticed in the liver of rats treated with HFD and α-LA. Our observations confirm that α-LA treatment has potential protective effects on inflammation development in the MASLD model. We believe that α-LA has a preventive impact when it comes to the progression of simple steatosis lesions to steatohepatitis.

Analysis of Influence of Cigarette Smoke on Signaling Pathways of Innate Immune System in Monocytes of Peripheral Blood

INTRODUCTION: Tobacco smoking is an important medical problem since it has a significant impact on the development and progression of chronic obstructive pulmonary disease (COPD). The components of tobacco smoke can initiate and support local and systemic inflammation with participation of monocytes and macrophages. AIM: To study molecular mechanisms associated with the impact of cigarette smoke on signaling pathways of the innate immune system in monocytes of peripheral blood. MATERIALS AND METHODS: The methods of in silico analysis was used to identify genes associated with the impact of tobacco smoke. On the basis of the data obtained, a cellular model of inflammation was created in vitro using tobacco smoke extract and monocytes of peripheral blood isolated by immunomagnetic separation. An enzyme-linked immunoassay (ELISA) kit was used to measure the concentration of tumor necrosis factor- (TNF-), interleukin-1 (IL-1) in cell supernatants, and of Toll-like receptor 4 (TLR4), ATP-binding cassette A1 (ABCA1) in homogenates of cell membranes of native monocytes and monocytes exposed to 4% tobacco smoke extract. These data were compared with the levels of TNF-, IL-1, TLR4 and ABCA1 in monocytes of peripheral blood of patients with COPD with frequent exacerbation phenotype and with obliterating atherosclerosis of lower limb arteries (OALLA). For statistical processing and visualization of the data, MedCalc 20.1.4 and R (version 4.2.2) software was used. RESULTS: Tobacco smoke influences TLR4, TNF- signaling pathways and lipid metabolism. Cigarette smoke extract enhanced the expression of proinflammatory cytokines TNF- and IL-1 in cell supernatants, increased the level of TLR4 and decreased that of ABCA1 in plasmolemma of monocytes of peripheral blood. In patients with COPD with frequent exacerbation phenotype and with OALLA, there were shown increase in the levels of proinflammatory TNF- and IL-1 cytokines in cell supernatants, increase in the level of TLR4 and reduction of the level of ABCA1 in plasmolemma of monocytes of peripheral blood compared to native monocytes of healthy individuals. CONCLUSION: Cigarette smoke enhances the production of proinflammatory TNF- and IL-1 cytokines, increases the levels of TLR4 protein and reduces the amount of ABCA1 transporter in membranes of monocytes of peripheral blood. This may partially explain the cause of the influence of cigarette smoke on development of the pulmonary and cardiovascular diseases. COPD with frequent exacerbation phenotype and OALLA are characterized by enhancement of inflammation with participation of monocytes.

Distinct Features of Vascular Diseases in COVID-19

The Coronavirus Disease 2019 (COVID-19) pandemic was declared in early 2020 after several unexplained pneumonia cases were first reported in Wuhan, China, and subsequently in other parts of the world. Commonly, the disease comprises several clinical features, including high temperature, dry cough, shortness of breath, and hypoxia, associated with findings of interstitial pneumonia on chest X-ray and computer tomography. Nevertheless, severe forms of acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) are not limited to the respiratory tract but also may be extended to other systems, including the cardiovascular system. The bi-directional relationship between atherosclerosis and COVID-19 is accompanied by poor prognosis. The immune response hyperactivation due to SARS-CoV-2 infection causes an increased secretion of cytokines, endothelial dysfunction, and arterial stiffness, which promotes the development of atherosclerosis. Also, due to the COVID-19 pandemic, access to healthcare amenities was reduced, resulting in increased morbidity and mortality in patients at risk. Furthermore, as lockdown measures were largely adopted worldwide, the sedentary lifestyle and the increased consumption of processed nutrients or unhealthy food increased, and in the consequence, we might observe even 70% of overweight and obese population. Altogether, with the relatively low ratio of vaccinated people in many countries, and important health debt appeared, which is now and will be for next decade a large healthcare challenge. However, the experience gained in the COVID-19 pandemic and the new methods of patients' approaching have helped the medical system to overcome this crisis and will hopefully help in the case of new possible epidemics.

HY, Kalin JH, Cole PA, Lassalle D, Forde-Thomas J, Chalmers IW, Brancale A, Grunau C, Hoffmann KF. Chemical modulation of Schistosoma mansoni lysine specific demethylase 1 (SmLSD1) induces wide-scale biological and epigenomic changes

Background: Schistosoma mansoni, a parasitic worm species responsible for the neglected tropical disease schistosomiasis, undergoes strict developmental regulation of gene expression that is carefully controlled by both genetic and epigenetic processes. As inhibition of S. mansoni epigenetic machinery components impairs key transitions throughout the parasite's digenetic lifecycle, a greater understanding of how epi-drugs affect molecular processes in schistosomes could lead to the development of new anthelmintics. Methods:   In vitro whole organism assays were used to assess the anti-schistosomal activity of 39 Homo sapiens Lysine Specific Demethylase 1 (HsLSD1) inhibitors on different parasite life cycle stages. Moreover, tissue-specific stains and genomic analysis shed light on the effect of these small molecules on the parasite biology. Results: Amongst this collection of small molecules, compound 33 was the most potent in reducing ex vivo viabilities of schistosomula, juveniles, miracidia and adults. At its sub-lethal concentration to adults (3.13 µM), compound 33 also significantly impacted oviposition, ovarian as well as vitellarian architecture and gonadal/neoblast stem cell proliferation. ATAC-seq analysis of adults demonstrated that compound 33 significantly affected chromatin structure (intragenic regions > intergenic regions), especially in genes differentially expressed in cell populations (e.g., germinal stem cells, hes2 + stem cell progeny, S1 cells and late female germinal cells) associated with these ex vivo phenotypes. KEGG analyses further highlighted that chromatin structure of genes associated with sugar metabolism as well as TGF-beta and Wnt signalling were also significantly perturbed by compound 33 treatment. Conclusions: This work confirms the importance of histone methylation in S. mansoni lifecycle transitions, suggesting that evaluation of LSD1 - targeting epi-drugs may facilitate the search for next-generation anti-schistosomal drugs. The ability of compound 33 to modulate chromatin structure as well as inhibit parasite survival, oviposition and stem cell proliferation warrants further investigations of this compound and its epigenetic target SmLSD1.