Altered microRNA profiles in bronchoalveolar lavage fluid exosomes in asthmatic patients

Extracellular vesicles and the lung: from disease pathogenesis to biomarkers and treatments

Nanosized extracellular vesicles (EVs) are released by all cells to convey cell-to-cell communication. EVs, including exosomes and microvesicles, carry an array of bioactive molecules, such as proteins and RNAs, encapsulated by a membrane lipid bilayer. Epithelial cells, endothelial cells, and various immune cells in the lung contribute to the pool of EVs in the lung microenvironment and carry molecules reflecting their cellular origin. EVs can maintain lung health by regulating immune responses, inducing tissue repair, and maintaining lung homeostasis. They can be detected in lung tissues and biofluids such as bronchoalveolar lavage fluid and blood, offering information about disease processes, and can function as disease biomarkers. Here, we discuss the role of EVs in lung homeostasis and pulmonary diseases such as asthma, chronic obstructive pulmonary disease, cystic fibrosis, pulmonary fibrosis, and lung injury. The mechanistic involvement of EVs in pathogenesis and their potential as disease biomarkers are discussed. Finally, the pulmonary field benefits from EVs as clinical therapeutics in severe pulmonary inflammatory disease, as EVs from mesenchymal stem cells attenuate severe respiratory inflammation in multiple clinical trials. Further, EVs can be engineered to carry therapeutic molecules for enhanced and broadened therapeutic opportunities, such as the anti-inflammatory molecule CD24. Finally, we discuss the emerging opportunity of using different types of EVs for treating severe respiratory conditions.

Key Amniotic Fluid miRNAs as Promising Target Molecules for the Antenatal Prevention of Pulmonary Hypoplasia Associated with Congenital Diaphragmatic Hernia

Congenital diaphragmatic hernia (CDH) remains associated with high morbidity and mortality, primarily due to pulmonary hypoplasia and hypertension. Current antenatal diagnostic methods, such as ultrasound and magnetic resonance imaging (MRI), are unable to assess the severity of defects in lung and pulmonary vascular structures, which are critical determinants of the diverse phenotypes of CDH. Aberrant epigenetic regulation of lung development during gestation is believed to play a significant role in the pathogenesis of CDH. In this study, we aimed to identify miRNA patterns in amniotic fluid capable of categorizing CDH-fetuses for the personalized selection of effective treatment strategies at the antenatal and/or postnatal stages. Using deep sequencing and quantitative real-time polymerase chain reaction (PCR), we identified a set of miRNAs-miR-485-3p, miR-320b, miR-320a-3p, miR-221-3p, miR-200b-3p, miR-100-5p, miR-92a-3p, miR-30c-5p, miR-26a-5p, and let-7c-5p-whose reduced expression in amniotic fluid at 19-24 weeks of gestation allowed us to categorize fetuses with CDH into two distinct groups: one significantly different from the control group (non-CDH) and the other closely resembling it. Notably, no significant correlations were found between the content of these miRNAs in amniotic fluid and severity of lung hypoplasia assessed by ultrasound or MRI. However, there was significant positive correlation between the level of each of the miRNAs with that of miR-200b-3p, whose role in ensuring proper bronchopulmonary tissue structure during prenatal development-as well as its therapeutic potential for CDH-associated hypoplastic lungs-has been previously demonstrated. These findings lay the groundwork for the future development of genetically engineered drug formulations designed for antenatal endotracheal administration to correct abnormal miRNA levels in lung tissue and mitigate the progression of pulmonary hypoplasia and hypertension in CDH-fetuses.

Exosomal Biomarkers: A Comprehensive Overview of Diagnostic and Prognostic Applications in Malignant and Non-Malignant Disorders

Exosomes are small extracellular vesicles, ranging from 30 to 150 nm, that are essential in cell biology, mediating intercellular communication and serving as biomarkers due to their origin from cells. Exosomes as biomarkers for diagnosing various illnesses have gained significant investigation due to the high cost and invasive nature of current diagnostic procedures. Exosomes have a clear advantage in the diagnosis of diseases because they include certain signals that are indicative of the genetic and proteomic profile of the ailment. This feature gives them the potential to be useful liquid biopsies for real-time, noninvasive monitoring, enabling early cancer identification for the creation of individualized treatment plans. According to our analysis, the trend toward utilizing exosomes as diagnostic and prognostic tools has raised since 2012. In this regard, the proportion of malignant indications is higher compared with non-malignant ones. To be precise, exosomes have been used the most in gastrointestinal, thoracic, and urogenital cancers, along with cardiovascular, diabetic, breathing, infectious, and brain disorders. To the best of our knowledge, this is the first research to examine all registered clinical trials that look at exosomes as a diagnostic and prognostic biomarker.

Role of Epigenetics in Chronic Lung Disease

Epigenetics regulates gene expression and thus cellular processes that underlie the pathogenesis of chronic lung diseases such as chronic obstructive pulmonary disease (COPD), asthma, and idiopathic pulmonary fibrosis (IPF). Environmental factors (e.g., air pollution, smoking, infections, poverty), but also conditions such as gastroesophageal reflux, induce epigenetic changes long before lung disease is diagnosed. Therefore, epigenetic signatures have the potential to serve as biomarkers that can be used to identify younger patients who are at risk for premature loss of lung function or diseases such as IPF. Epigenetic analyses also contribute to a better understanding of chronic lung disease. This can be used directly to improve therapies, as well as for the development of innovative drugs. Here, we highlight the role of epigenetics in the development and progression of chronic lung disease, with a focus on DNA methylation.

Comparison of nanoLC-MALDI-MS/MS with nanoLC-TIMS-MS/MS in the proteomic analysis of extracellular vesicles of bronchoalveolar lavage fluid

The study aims to evaluate and compare two advanced proteomic techniques, nanoLC-MALDI-MS/MS and nanoLC-TIMS-MS/MS, in characterizing extracellular vesicles (EVs) from the bronchoalveolar lavage fluid (BALF) of patients with asthma and idiopathic pulmonary fibrosis (IPF). Pulmonary diseases, driven by pollutants and infections, often necessitate detailed analysis of BALF to identify diagnostic biomarkers and therapeutic targets. EVs, which include exosomes, microvesicles, and apoptotic bodies, are isolated using filtration and ultracentrifugation, and their morphology, concentration, and size distribution are assessed through transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). The proteomic profiles of these EVs are then analyzed using the aforementioned techniques, highlighting their unique and common proteins. The study found that nanoLC-TIMS-MS/MS identified significantly more proteins compared to nanoLC-MALDI-MS/MS. Functional analysis via Gene Ontology revealed pathways related to inflammation and cell signaling, underscoring the role of EVs in disease pathophysiology. The findings suggest that EVs in BALF can serve as valuable biomarkers and therapeutic targets in respiratory diseases, providing a foundation for future research and clinical applications.

Plasma extracellular vesicles regulate the Functions of Th2 and ILC2 cells via miRNA-150-5p in patients with allergic rhinitis

Allergic rhinitis (AR), a chronic airway inflammation, has witnessed a rising prevalence in recent decades. Recent research indicates that various EVs are released into plasma in allergic airway inflammation, correlating with impaired airway function and severe inflammation. However, the contribution of plasma EVs to AR pathogenesis remains incompletely understood. We isolated plasma EVs using differential ultracentrifugation or size exclusion chromatography (SEC) and obtained differential microRNA (miRNA) expression profiles through miRNA sequencing. Peripheral blood mononuclear cells (PBMCs) were exposed to plasma EVs and miRNA mimics and inhibitors to assess the effect of plasma EVs and the underlying mechanisms. We found that EVs from HC and AR patients exhibited comparable characteristics in terms of concentration, structure, and EV marker expression. AR-EVs significantly enhanced Th2 cell levels and promoted ILC2 differentiation and IL-13+ ILC2 levels compared to HC-EVs. Both HC-EVs and AR-EVs were efficiently internalized by CD4+ T cells and ILCs. miRNA sequencing of AR-EVs revealed unique miRNA signatures implicated in diverse biological processes, among which miR-150-5p, miR-144-3p, miR-10a-5p, and miR-10b-5p were identified as pivotal contributors to AR-EVs' effects on CD4+ T cells and ILC2s. MiR-150-5p exhibited the most pronounced impact on cell differentiation and was confirmed to be upregulated in AR-EVs by PCR. In total, our study demonstrated that plasma EVs from patients with AR exhibited a pronounced capacity to significantly enhance the differentiation of Th2 cells and ILC2, which was correlated with an elevated expression of miR-150-5p within AR-EVs. These findings contribute to the advancement of our comprehension of EVs in the pathogenesis of AR and hold the potential to unveil novel therapeutic targets for the treatment of AR.

Extracellular vesicles transport RNA between cells: Unraveling their dual role in diagnostics and therapeutics

Modern methods of molecular diagnostics and therapy have revolutionized the field of medicine in recent years by providing more precise and effective tools for detecting and treating diseases. This progress includes a growing exploration of the body's secreted vesicles, known as extracellular vesicles (EVs), for both diagnostic and therapeutic purposes. EVs are a heterogeneous population of lipid bilayer vesicles secreted by almost every cell type studied so far. They are detected in body fluids and conditioned culture media from living cells. EVs play a crucial role in communication between cells and organs, both locally and over long distances. They are recognized for their ability to transport endogenous RNA and proteins between cells, including messenger RNA (mRNA), microRNA (miRNA), misfolded neurodegenerative proteins, and several other biomolecules. This review explores the dual utilization of EVs, serving not only for diagnostic purposes but also as a platform for delivering therapeutic molecules to cells and tissues. Through an exploration of their composition, biogenesis, and selective cargo packaging, we elucidate the intricate mechanisms behind RNA transport between cells via EVs, highlighting their potential use for both diagnostic and therapeutic applications. Finally, it addresses challenges and outlines prospective directions for the clinical utilization of EVs.

Roles of Exosomal miRNAs in Asthma: Mechanisms and Applications

Asthma is a chronic inflammatory disorder of the airways, characterized by a complex interplay of genetic, environmental, and immunological factors that contribute to its onset and progression. Recent advances in researches have illuminated the critical role of exosomal microRNAs (miRNAs) in the pathogenesis and development of asthma. Exosomes are nano-sized extracellular vesicles that facilitate intercellular communication by transporting a variety of bioactive molecules, including miRNAs, and play a crucial role in regulating gene expression and immune responses, which are central to the inflammatory processes underlying asthma. Exosomal miRNAs are emerging as key players in asthma due to their involvement in various aspects of the disease, including the regulation of inflammation, airway hyperresponsiveness, and remodeling. Their ability to influence the behavior of target cells and tissues makes them valuable both as diagnostic biomarkers and as potential therapeutic targets. This review aims to provide a comprehensive overview of the biogenesis of exosomes, the functional roles of exosomal miRNAs in asthma, and their clinical potential. It will explore the mechanisms by which these miRNAs contribute to asthma pathophysiology, discuss their utility in diagnosing and monitoring the disease, and highlight ongoing research efforts to harness their therapeutic potential.

Specific microRNA Profile Associated with Inflammation and Lipid Metabolism for Stratifying Allergic Asthma Severity

The mechanisms underlying severe allergic asthma are complex and unknown, meaning it is a challenge to provide the most appropriate treatment. This study aimed to identify novel biomarkers for stratifying allergic asthmatic patients according to severity, and to uncover the biological mechanisms that lead to the development of the severe uncontrolled phenotype. By using miRNA PCR panels, we analyzed the expression of 752 miRNAs in serum samples from control subjects (n = 15) and mild (n = 11) and severe uncontrolled (n = 10) allergic asthmatic patients. We identified 40 differentially expressed miRNAs between severe uncontrolled and mild allergic asthmatic patients. Functional enrichment analysis revealed signatures related to inflammation, angiogenesis, lipid metabolism and mRNA regulation. A random forest classifier trained with DE miRNAs achieved a high accuracy of 97% for severe uncontrolled patient stratification. Validation of the identified biomarkers was performed on a subset of allergic asthmatic patients from the CAMP cohort at Brigham and Women's Hospital, Harvard Medical School. Four of these miRNAs (hsa-miR-99b-5p, hsa-miR-451a, hsa-miR-326 and hsa-miR-505-3p) were validated, pointing towards their potential as biomarkers for stratifying allergic asthmatic patients by severity and providing insights into severe uncontrolled asthma molecular pathways.

Extracellular Vesicle microRNA: A Promising Biomarker and Therapeutic Target for Respiratory Diseases

Respiratory diseases, including chronic obstructive pulmonary disease (COPD), asthma, lung cancer, and coronavirus pneumonia, present a major global health challenge. Current diagnostic and therapeutic options for these diseases are limited, necessitating the urgent development of novel biomarkers and therapeutic strategies. In recent years, microRNAs (miRNAs) within extracellular vesicles (EVs) have received considerable attention due to their crucial role in intercellular communication and disease progression. EVs are membrane-bound structures released by cells into the extracellular environment, encapsulating a variety of biomolecules such as DNA, RNA, lipids, and proteins. Specifically, miRNAs within EVs, known as EV-miRNAs, facilitate intercellular communication by regulating gene expression. The expression levels of these miRNAs can reflect distinct disease states and significantly influence immune cell function, chronic airway inflammation, airway remodeling, cell proliferation, angiogenesis, epithelial-mesenchymal transition, and other pathological processes. Consequently, EV-miRNAs have a profound impact on the onset, progression, and therapeutic responses of respiratory diseases, with great potential for disease management. Synthesizing the current understanding of EV-miRNAs in respiratory diseases such as COPD, asthma, lung cancer, and novel coronavirus pneumonia, this review aims to explore the potential of EV-miRNAs as biomarkers and therapeutic targets and examine their prospects in the diagnosis and treatment of these respiratory diseases.

Th2 cell extracellular vesicles promote eosinophil survival through the cytokine cargo IL-3 and prolong airway eosinophilia

Background

Extracellular vesicles (EVs) mediate intercellular communication during immune responses. EVs are abundant in respiratory biofluids, and the composition of EVs in the lung changes during inflammation.

Objective

We aimed to quantify the contribution of T cells to airway EVs in allergic lung inflammation and ascertain their function during a type 2 inflammatory response.

Methods

Genetic membrane tagging was combined with single vesicle flow cytometry to quantify T cell EVs in the airways of mice challenged with ovalbumin or house dust mite. EVs were purified from T helper type 2 (Th2) cell cultures and their functions on eosinophils assessed by flow cytometry and RNA sequencing. Th2 cell EVs were instilled into the lungs of mice to determine effects on lung eosinophilia. Finally, the function of an EV protein cargo was tested using inhibitors and blocking antibodies.

Results

T cell EVs are increased in the airways of mice with induced allergic inflammation. EVs secreted by Th2 cells inhibit apoptosis and induce activating pathways in eosinophils in vitro. This effect depends on re-stimulation through the T cell receptor. Th2 cell EVs prolong eosinophilia in vivo during allergic airway inflammation. Th2 cell EVs carry a potent form of the cytokine IL-3 on their surfaces, which inhibits apoptosis by activating Jak1/2-dependent pro-survival programs in eosinophils.

Conclusion

Th2 cell EVs promote eosinophil survival and prolong eosinophilia during allergic airway inflammation. This function depends on the EV cargo IL-3, supporting a role for EVs as vehicles of cytokine-based communication in lung inflammation.

Key Messages

T cells secrete extracellular vesicles in the airway during allergic lung inflammation.Th2 cell extracellular vesicles inhibit eosinophil apoptosis and prolong airway eosinophilia during allergic lung inflammation.IL-3 carried on Th2 cell EVs is a functional cargo, supporting a role for cytokine-carrying EVs as drivers of type 2 inflammation.

Capsule summary

This study supports that T cell extracellular vesicles may be important drivers of eosinophilic inflammation through the cytokine cargo IL-3, offering new insights into pro-inflammatory signaling in the allergic lung of patients with asthma.

Extracellular vesicle miRNAs drive aberrant macrophage responses in NSAID-exacerbated respiratory disease

BACKGROUND

Extracellular vesicles (EVs) have been implicated in the pathogenesis of asthma, however, how EVs contribute to immune dysfunction and type 2 airway inflammation remains incompletely understood. We aimed to elucidate roles of airway EVs and their miRNA cargo in the pathogenesis of NSAID-exacerbated respiratory disease (N-ERD), a severe type 2 inflammatory condition.

METHODS

EVs were isolated from induced sputum or supernatants of cultured nasal polyp or turbinate tissues of N-ERD patients or healthy controls by size-exclusion chromatography and characterized by particle tracking, electron microscopy and miRNA sequencing. Functional effects of EV miRNAs on gene expression and mediator release by human macrophages or normal human bronchial epithelial cells (NHBEs) were studied by RNA sequencing, LC-MS/MS and multiplex cytokine assays.

RESULTS

EVs were highly abundant in secretions from the upper and lower airways of N-ERD patients. N-ERD airway EVs displayed profoundly altered immunostimulatory capacities and miRNA profiles compared to airway EVs of healthy individuals. Airway EVs of N-ERD patients, but not of healthy individuals induced inflammatory cytokine (GM-CSF and IL-8) production by NHBEs. In macrophages, N-ERD airway EVs exhibited an impaired potential to induce cytokine and prostanoid production, while enhancing M2 macrophage activation. Let-7 family miRNAs were highly enriched in sputum EVs from N-ERD patients and mimicked suppressive effects of N-ERD EVs on macrophage activation.

CONCLUSION

Aberrant airway EV miRNA profiles may contribute to immune dysfunction and chronic type 2 inflammation in N-ERD. Let-7 family miRNAs represent targets for correcting aberrant macrophage activation and mediator responses in N-ERD.

High-throughput proteomic analysis of extracellular vesicles from saliva by chemical probe-based array

Extracellular vesicles (EVs) are cell-released, nucleus-free particles with a double-membrane structure that effectively prevents degradation of internal components by a variety of salivary enzymes. Saliva is an easily accessible biofluid that contains a wealth of valuable information for disease diagnosis and monitoring and especially reflect respiratory and digestive tract diseases. However, the lack of efficient and high-throughput methods for proteomic analysis of salivary biomarkers poses a significant challenge. Herein, we designed a salivary EV amphiphile-dendrimer supramolecular probe (SEASP) array which enables efficient enrichment and in situ detection of EVs protein biomarkers. Detergent Tween-20 washing of SEASP arrays removes high abundance of heteroproteins from saliva well. This array shows good analytical performance in the linear range of 10 μL-150 μL (LOD = 0.4 μg protein, or 10 μL saliva), exhibiting a good recovery (80.0 %). Compared to ultracentrifugation (UC), this procedure provides simple and convenient access to high-purity EVs (1.3 × 109 particles per mg protein) with good physiological status and structure. Coupling with mass spectrometry based proteomic analysis, differentially expressed proteins as selected asthma biomarkers have been screened. Then, we validated the proteomics primary screening results through clinical samples (100 μL each) using the SEASP array. Utilizing the dual antibody fluorescence technology, SEASP enables the simultaneous high-throughput detection of two proteins. Therefore, the EVs marker protein CD81 could be used as an internal standard to normalize the number of EVs, which was stably expressed in EVs. Proteomics and array results suggested that HNRNPU (P = 4.9 * 10-6) and MUC5B (P = 4.7 * 10-11) are promising protein biomarkers for infantile asthma. HNRNPU and MUC5B may be associated with disease onset and subtypes. The SEASP arrays provide a significant advancement in the field of salivary biomarker. The array enables high-throughput in situ protein detection for highly viscous and complex biological samples. It provides a rapid, low-cost, highly specific screening procedure and experimental basis for early disease screening and diagnosis in the field of liquid biopsy.

Exosomes in asthma: Underappreciated contributors to the pathogenesis and novel therapeutic tools

OBJECTIVE

Asthma, a chronic inflammatory disease with diverse pathomechanisms, presents challenges in developing personalized diagnostic and therapeutic approaches. This review aims to provide a comprehensive overview of the role of exosomes, small extracellular vesicles, in asthma pathophysiology and explores their potential as diagnostic biomarkers and therapeutic tools.

METHODS

A literature search was conducted to identify recent studies investigating the involvement of exosomes in asthma. The retrieved articles were analyzed to extract relevant information on the role of exosomes in maintaining lung microenvironment homeostasis, regulating inflammatory responses, and their diagnostic and therapeutic potential for asthma.

RESULTS

Exosomes secreted by various cell types, have emerged as crucial mediators of intercellular communication in healthy and diseased conditions. Evidence suggest that exosomes play a significant role in maintaining lung microenvironment homeostasis and contribute to asthma pathogenesis by regulating inflammatory responses. Differential exosomal content between healthy individuals and asthmatics holds promise for the development of novel asthma biomarkers. Furthermore, exosomes secreted by immune and nonimmune cells, as well as those detected in biofluids, demonstrate potential in promoting or regulating immune responses, making them attractive candidates for designing new treatment strategies for inflammatory conditions such as asthma.

CONCLUSION

Exosomes, with their ability to modulate immune responses and deliver therapeutic cargo, offer potential as targeted therapeutic tools in asthma management. Further research and clinical trials are required to fully understand the mechanisms underlying exosome-mediated effects and translate these findings into effective diagnostic and therapeutic strategies for asthma patients.

The New Paradigm: The Role of Proteins and Triggers in the Evolution of Allergic Asthma

Epithelial barrier damage plays a central role in the development and maintenance of allergic inflammation. Rises in the epithelial barrier permeability of airways alter tissue homeostasis and allow the penetration of allergens and other external agents. Different factors contribute to barrier impairment, such as eosinophilic infiltration and allergen protease action-eosinophilic cationic proteins' effects and allergens' proteolytic activity both contribute significantly to epithelial damage. In the airways, allergen proteases degrade the epithelial junctional proteins, allowing allergen penetration and its uptake by dendritic cells. This increase in allergen-immune system interaction induces the release of alarmins and the activation of type 2 inflammatory pathways, causing or worsening the main symptoms at the skin, bowel, and respiratory levels. We aim to highlight the molecular mechanisms underlying allergenic protease-induced epithelial barrier damage and the role of immune response in allergic asthma onset, maintenance, and progression. Moreover, we will explore potential clinical and radiological biomarkers of airway remodeling in allergic asthma patients.

Tuning into miRNAs: A comprehensive analysis of their impact on diagnosis, and progression in asthma

Asthma is a diverse inflammatory illness affecting the respiratory passages, leading to breathing challenges, bouts of coughing and wheezing, and, in severe instances, significant deterioration in quality of life. Epigenetic regulation, which involves the control of gene expression through processes such as post-transcriptional modulation of microRNAs (miRNAs), plays a role in the evolution of various asthma subtypes. In immune-mediated diseases, miRNAs play a regulatory role in the behavior of cells that form the airway structure and those responsible for defense mechanisms in the bronchi and lungs. They control various cellular processes such as survival, growth, proliferation, and the production of chemokines and immune mediators. miRNAs possess chemical and biological characteristics that qualify them as suitable biomarkers for diseases. They allow for the categorization of patients to optimize drug selection, thus streamlining clinical management and decreasing both the economic burden and the necessity for critical care related to the disease. This study provides a concise overview of the functions of miRNAs in asthma and elucidates their regulatory effects on the underlying processes of the disease. We provide a detailed account of the present status of miRNAs as biomarkers for categorizing asthma, identifying specific asthma subtypes, and selecting appropriate treatment options.

Diagnostic and therapeutic value of EVs in lungs diseases and inflammation

Extracellular vesicles (EVs) are membrane-derived messengers which have been playing an important role in the inflammation and pathogenesis of lung diseases. EVs contain varieties of DNA, RNA, and membrane receptors through which they work as a delivery system for bioactive molecules as well as intracellular communicators. EV signaling mediates tumor progression and metastasis. EVs are linked with many diseases and perform a diagnostic role in lung injury and inflammation so are used to diagnose the severity of diseases. EVs containing a variety of biomolecules communicate with the recipient cells during pathophysiological mechanisms thereby acquiring the attention of clinicians toward the diagnostic and therapeutic potential of EVs in different lung diseases. In this review, we summarize the role of EVs in inflammation with an emphasis on their potential as a novel candidate in the diagnostics and therapeutics of chronic obstructive pulmonary disease, asthma, and sarcoidosis.

Emerging applications of extracellular vesicles in tumor therapy

Extracellular vesicles (EVs) have tremendous potential as nano/micron-sized drug delivery carriers. Their physical, chemical and biological characteristics distinguish them as unique carriers with specific pharmacokinetic, circulating metabolic, and biodistribution patterns in the delivery of therapeutic cargoes. They are critical mediators in the pathology of many diseases, including inflammatory diseases, fibrosis, and cancer, but they are also essential mediators in immunomodulation, cancer treatment, infectious defense, and tissue repair. In this review, we emphasize recent advances in oncology therapy using macrophage EVs, mesenchymal stem cell EVs, milk EVs, and plant EVs, as well as the advantages of EVs as delivery platforms and their prospective clinical applications and use.

Consensus clustering with missing labels (ccml): a consensus clustering tool for multi-omics integrative prediction in cohorts with unequal sample coverage

Multi-omics data integration is a complex and challenging task in biomedical research. Consensus clustering, also known as meta-clustering or cluster ensembles, has become an increasingly popular downstream tool for phenotyping and endotyping using multiple omics and clinical data. However, current consensus clustering methods typically rely on ensembling clustering outputs with similar sample coverages (mathematical replicates), which may not reflect real-world data with varying sample coverages (biological replicates). To address this issue, we propose a new consensus clustering with missing labels (ccml) strategy termed ccml, an R protocol for two-step consensus clustering that can handle unequal missing labels (i.e. multiple predictive labels with different sample coverages). Initially, the regular consensus weights are adjusted (normalized) by sample coverage, then a regular consensus clustering is performed to predict the optimal final cluster. We applied the ccml method to predict molecularly distinct groups based on 9-omics integration in the Karolinska COSMIC cohort, which investigates chronic obstructive pulmonary disease, and 24-omics handprint integrative subgrouping of adult asthma patients of the U-BIOPRED cohort. We propose ccml as a downstream toolkit for multi-omics integration analysis algorithms such as Similarity Network Fusion and robust clustering of clinical data to overcome the limitations posed by missing data, which is inevitable in human cohorts consisting of multiple data modalities. The ccml tool is available in the R language (https://CRAN.R-project.org/package=ccml, https://github.com/pulmonomics-lab/ccml, or https://github.com/ZhoulabCPH/ccml).

Role of exosomes in the development, diagnosis, prognosis and treatment of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most common primary liver cancer. It is characterized by occult onset resulting in most patients being diagnosed at advanced stages and with poor prognosis. Exosomes are nanoscale vesicles with a lipid bilayer envelope released by various cells under physiological and pathological conditions, which play an important role in the biological information transfer between cells. There is growing evidence that HCC cell-derived exosomes may contribute to the establishment of a favorable microenvironment that supports cancer cell proliferation, invasion, and metastasis. These exosomes not only provide a versatile platform for diagnosis but also serve as a vehicle for drug delivery. In this paper, we review the role of exosomes involved in the proliferation, migration, and metastasis of HCC and describe their application in HCC diagnosis and treatment. We also discuss the prospects of exosome application in HCC and the research challenges.

Exosomal microRNA/miRNA Dysregulation in Respiratory Diseases: From Mycoplasma-Induced Respiratory Disease to COVID-19 and Beyond

Respiratory diseases represent a significant economic and health burden worldwide, affecting millions of individuals each year in both human and animal populations. MicroRNAs (miRNAs) play crucial roles in gene expression regulation and are involved in various physiological and pathological processes. Exosomal miRNAs and cellular miRNAs have been identified as key regulators of several immune respiratory diseases, such as chronic respiratory diseases (CRD) caused by Mycoplasma gallisepticum (MG), Mycoplasma pneumoniae pneumonia (MMP) caused by the bacterium Mycoplasma pneumoniae, coronavirus disease 2019 (COVID-19), chronic obstructive pulmonary disease (COPD), asthma, and acute lung injury/acute respiratory distress syndrome (ALI/ARDS). Consequently, miRNAs seem to have the potential to serve as diagnostic biomarkers and therapeutic targets in respiratory diseases. In this review, we summarize the current understanding of the functional roles of miRNAs in the above several respiratory diseases and discuss the potential use of miRNAs as stable diagnostic biomarkers and therapeutic targets for several immune respiratory diseases, focusing on the identification of differentially expressed miRNAs and their targeting of various signaling pathways implicated in disease pathogenesis. Despite the progress made, unanswered questions and future research directions are discussed to facilitate personalized and targeted therapies for patients with these debilitating conditions.

Exosome miR-223-3p in the bone marrow-derived mesenchymal stem cells alleviates the inflammation and airway remodeling through NLRP3-induced ASC/Caspase-1/GSDMD signaling pathway

Asthma is one of the most common chronic respiratory diseases in the world. Exploration and understanding of the pathogenesis of epithelial-mesenchymal transition in airway epithelial cells, and the development of new molecular drugs targeted at airway inflammation and remodeling have become the key and hot points in the prevention and treatment of asthma. Emerging evidence has proven that miRNAs are strongly associated with numerous chronic respiratory diseases including asthma, but the involved molecular mechanisms have not been revealed. In the present study, we successfully isolated exosomes from BMMSCs and found that the derived exosomes could improve airway inflammation and remodeling in ovalbumin-induced asthma rats. Furthermore, we found that the highly expressed miR-223-3p in exosomes might play a key pivotal role in the protective effects on airway remodeling and asthma by regulating the NLRP3-induced ASC/Caspase-1/GSDMD signaling pathway. These results provided a promising molecule candidate and target for the therapy of asthma.

Research trends and hotspots of exosomes in respiratory diseases

Currently, theoretical studies on exosomes in respiratory diseases have received much attention from many scholars and have made remarkable progress, which has inestimable value and potential in future clinical and scientific research. Unfortunately, no scholar has yet addressed this field's bibliometric analysis and summary. We aim to comprehensively and profoundly study and explore the present situation and highlights of exosome research at the stage of respiratory diseases and to provide meaningful insights for the future development of this field. The WOSCC literature was gathered for the study using bibliometrics, and the data were collected and analyzed using CiteSpace, VOSviewer, Microsoft Excel, and Endnote software. The publication language is "English," and the search strategy is TS = (exosome OR exosomes OR exosomal) AND TS = (respiratory OR lung). The search time is from the beginning of the WOS construction, and the deadline is July 11, 2022, at 22:00 hours. The literature types selected were dissertation, review paper, and online published paper. The analysis includes 2456 publications in 738 journals from 76 countries, 2716 institutions, and 14,568 authors. The field's annual publications have been rising, especially in recent years. China and the US lead research, and prominent universities, including Harvard Medical School, Shanghai Jiao Tong University, and Fudan University, are essential research institutes. Takahiro Ochiya, whose research focuses on exosomes and lung cancer, and Clotilde Théry, a pioneering exosome researcher, are the most cited authors in this field. The key terms include lung cancer, non-small cell lung cancer, mesenchymal stem cells, intercellular communication, exosomal miRNAs, and oncology. Cell biology, biochemistry & biotechnology, and oncology are related fields. The final summary of research hotspots is exosomes and lung cancer, mesenchymal stem cell-derived exosomes and lung inflammation, and miRNAs in exosomes as biomarkers for respiratory illnesses. The present research situation and relevant hotspots of the area were analyzed through bibliometric studies on exosomes in respiratory diseases. The research development in this field has a considerable upside, and the exosome's function in diagnosing, treating, monitoring, and prognosis of respiratory illnesses cannot be taken lightly. Moreover, we believe the research results will bring the gospel to many patients with clinical respiratory diseases shortly.

Extracellular Vesicles (EVs) as Crucial Mediators of Cell-Cell Interaction in Asthma

Asthma is the most common chronic respiratory disorder worldwide and accounts for a huge health and economic burden. Its incidence is rapidly increasing but, in parallel, novel personalized approaches have emerged. Indeed, the improved knowledge of cells and molecules mediating asthma pathogenesis has led to the development of targeted therapies that significantly increased our ability to treat asthma patients, especially in severe stages of disease. In such complex scenarios, extracellular vesicles (EVs i.e., anucleated particles transporting nucleic acids, cytokines, and lipids) have gained the spotlight, being considered key sensors and mediators of the mechanisms controlling cell-to-cell interplay. We will herein first revise the existing evidence, mainly by mechanistic studies in vitro and in animal models, that EV content and release is strongly influenced by the specific triggers of asthma. Current studies indicate that EVs are released by potentially all cell subtypes in the asthmatic airways, particularly by bronchial epithelial cells (with different cargoes in the apical and basolateral side) and inflammatory cells. Such studies largely suggest a pro-inflammatory and pro-remodelling role of EVs, whereas a minority of reports indicate protective effects, particularly by mesenchymal cells. The co-existence of several confounding factors-including technical pitfalls and host and environmental confounders-is still a major challenge in human studies. Technical standardization in isolating EVs from different body fluids and careful selection of patients will provide the basis for obtaining reliable results and extend their application as effective biomarkers in asthma.

Non-Coding RNAs in Pulmonary Diseases: Comparison of Different Airway-Derived Biosamples

Due to their structural conservation and functional role in critical signalling pathways, non-coding RNA (ncRNA) is a promising biomarker and modulator of pathological conditions. Most research has focussed on the role of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These molecules have been investigated both in a cellular and an extracellular context. Sources of ncRNAs may include organ-specific body fluids. Therefore, studies on ncRNAs in respiratory diseases include those on sputum, bronchoalveolar lavage fluid (BALF) and exhaled breath condensate (EBC). It is worth identifying the limitations of these biosamples in terms of ncRNA abundance, processing and diagnostic potential. This review describes the progress in the literature on the role of ncRNAs in the pathogenesis and progression of severe respiratory diseases, including cystic fibrosis, asthma and interstitial lung disease. We showed that there is a deficit of information on lncRNAs and circRNAs in selected diseases, despite attempts to functionally bind them to miRNAs. miRNAs remain the most well-studied, but only a few investigations have been conducted on the least invasive biosample material, i.e., EBC. To summarise the studies conducted to date, we also performed a preliminary in silico analysis of the reported miRNAs, demonstrating the complexity of their role and interactions in selected respiratory diseases.

Advances and Highlights of miRNAs in Asthma: Biomarkers for Diagnosis and Treatment

Asthma is a heterogeneous inflammatory disease of the airways that causes breathing difficulties, episodes of cough and wheezing, and in more severe cases can greatly diminish quality of life. Epigenetic regulation, including post-transcriptional mediation of microRNAs (miRNAs), is one of the mechanisms behind the development of the range of asthma phenotypes and endotypes. As in every other immune-mediated disease, miRNAs regulate the behavior of cells that shape the airway structure as well as those in charge of the defense mechanisms in the bronchi and lungs, controlling cell survival, growth, proliferation, and the ability of cells to synthesize and secrete chemokines and immune mediators. More importantly, miRNAs are molecules with chemical and biological properties that make them appropriate biomarkers for disease, enabling stratification of patients for optimal drug selection and thereby simplifying clinical management and reducing both the economic burden and need for critical care associated with the disease. In this review, we summarize the roles of miRNAs in asthma and describe how they regulate the mechanisms of the disease. We further describe the current state of miRNAs as biomarkers for asthma phenotyping, endotyping, and treatment selection.

The impact of environmental contaminants on extracellular vesicles and their key molecular regulators: A literature and database-driven review

Exposure to environmental chemicals is now well recognized as a significant factor contributing to the global burden of disease; however, there remain critical gaps in understanding the types of biological mechanisms that link environmental chemicals to adverse health outcomes. One type of mechanism that remains understudied involves extracellular vesicles (EVs), representing small cell-derived particles capable of carrying molecular signals such as RNAs, miRNAs, proteins, lipids, and chemicals through biological fluids and imparting beneficial, neutral, or negative effects on target cells. In fact, evidence is just now starting to grow that supports the role of EVs in various disease etiologies. This review aims to (1) Provide a landscape of the current understanding of the functional relationship between EVs and environmental chemicals; (2) Summarize current knowledge of EV regulatory processes including production, packaging, and release; and (3) Conduct a database-driven analysis of known chemical-gene interactions to predict and prioritize environmentally relevant chemicals that may impact EV regulatory genes and thus EV regulatory processes. This approach to predicting environmentally relevant chemicals that may alter EVs provides a novel method for evidence-based hypothesis generation for future studies evaluating the link between environmental exposures and EVs.

Extracellular vesicles derived from macrophages: Current applications and prospects in tumors

Macrophages (Mφs) are significant innate immune cells that perform a variety of tasks in response to different pathogens or stimuli. They are widely engaged in the pathological processes of various diseases and can contribute to tumorigenesis, progression and metastasis by regulating the tumor microenvironment and cancer cells. They are also the basis of chemoresistance. In turn, the tumor microenvironment and the metabolism of cancer cells can limit the differentiation, polarization, mobilization and the ability of Mφs to initiate an effective anti-tumor response. Extracellular vesicles (EVs) are small vesicles released by live cells that serve as crucial mediators of intercellular cell communication as well as a potential promising drug carrier. A growing number of studies have demonstrated that Mφs-EVs are not only important mediators in the pathological processes of various diseases such as inflammatory disorders, fibrosis and cancer, but also show significant potential in immunological modulation, cancer therapy, infectious defense and tissue repair. These natural nanoparticles (NPs) derived from Mφs are believed to be pleiotropic, stable, biocompatible and low immunogenic, providing novel alternatives for cancer treatment. This review provides an update on the pathological and therapeutic roles of Mφs-EVs in cancer, as well as their potential clinical applications and prospects.

Pulmonary EV miRNA profiles identify disease and distinct inflammatory endotypes in COPD

Introduction

Chronic obstructive pulmonary disease (COPD) is a heterogeneous condition without effective disease modifying therapies. Identification of novel inflammatory endotype markers such as extracellular vesicles (EVs), which are important intercellular messengers carrying microRNA (miRNA), may enable earlier diagnosis and disease stratification for a targeted treatment approach. Our aim was to identify differentially expressed EV miRNA in the lungs of COPD patients compared with healthy ex-smokers and determine whether they can help define inflammatory COPD endotypes.

Methods

EV miRNA were isolated and sequenced from ex-smoking COPD patients and healthy ex-smoker bronchoalveolar lavage fluid. Results were validated with RT-qPCR and compared to differential inflammatory cell counts.

Results

Expression analysis identified five upregulated miRNA in COPD (miR-223-3p, miR-2110, miR-182-5p, miR-200b-5p and miR-625-3p) and three downregulated miRNA (miR-138-5p, miR-338-3p and miR-204-5p), all with a log2 fold change of >1/-1, FDR < 0.05. These miRNAs correlated with disease defining characteristics such as FEF 25-75% (a small airways disease measure) and DLCO% (a surrogate measure of emphysema). Receiver operator curve analysis demonstrated miR-2110, miR-223-3p, and miR-182-5p showed excellent combinatory predictive ability (AUC 0.91, p < 0.0001) in differentiating between health and mild COPD. Furthermore, miR-223-3p and miR-338-3p correlated with airway eosinophilia and were able to distinguish "pure eosinophilic" COPD from other airway inflammatory subtypes (AUC 0.94 and 0.85, respectively).

Discussion

This is the first study to identify differentially expressed miRNA in COPD bronchoalveolar lavage fluid EVs. These findings suggest specific lung derived EV miRNA are a strong predictor of disease presence even in mild COPD. Furthermore, specific miRNA correlated with inflammatory cell numbers in COPD, and may have a role in defining inflammatory endotypes for future treatment stratification.

Emerging role of mesenchymal stem cell-derived extracellular vesicles in oral and craniomaxillofacial tissue regenerative medicine

Mesenchymal stem cells (MSCs) are multipotent stem cells with differentiation potential and paracrine properties, drawing significant attention in the field of regenerative medicine. Extracellular vesicles (EVs), mainly including exosomes, microvesicles and apoptotic bodies (ABs), are predominantly endosomal in origin and contain bioactive molecules, such as miRNAs, mRNAs, and proteins, which are transferred from their original cells to target cells. Recently it has emerged that MSC-derived EVs (MSC-EVs) combine the advantages of MSCs and EVs, which may be used as a promising MSC-based therapy in tissue repair and regeneration. Oral and craniomaxillofacial diseases are clinically complications containing the soft and hard tissues in craniofacial and dental arches. These diseases are often induced by various factors, such as chemical, microbiological, physical factors, and systemic disorders. For decades, tissue repair and regeneration in oral and craniomaxillofacial regions provide substantial improvements in the prevention and treatment of some severe diseases. In this review we discuss MSC-EVs and their therapeutic potential in oral and craniomaxillofacial tissue regenerative medicine.

miRNA-mRNA-protein dysregulated network in COPD in women

Rationale: Chronic obstructive pulmonary disease (COPD) is a complex disease caused by a multitude of underlying mechanisms, and molecular mechanistic modeling of COPD, especially at a multi-molecular level, is needed to facilitate the development of molecular diagnostic and prognostic tools and efficacious treatments. Objectives: To investigate the miRNA-mRNA-protein dysregulated network to facilitate prediction of biomarkers and disease subnetwork in COPD in women. Measurements and Results: Three omics data blocks (mRNA, miRNA, and protein) collected from BAL cells from female current-smoker COPD patients, smokers with normal lung function, and healthy never-smokers were integrated with miRNA-mRNA-protein regulatory networks to construct a COPD-specific dysregulated network. Furthermore, downstream network topology, literature annotation, and functional enrichment analysis identified both known and novel disease-related biomarkers and pathways. Both abnormal regulations in miRNA-induced mRNA transcription and protein translation repression play roles in COPD. Finally, the let-7-AIFM1-FKBP1A pathway is highlighted in COPD pathology. Conclusion: For the first time, a comprehensive miRNA-mRNA-protein dysregulated network of primary immune cells from the lung related to COPD in females was constructed to elucidate specific biomarkers and disease pathways. The multi-omics network provides a new molecular insight from a multi-molecular aspect and highlights dysregulated interactions. The highlighted let-7-AIFM1-FKBP1A pathway also indicates new hypotheses of COPD pathology.

EVs-miRNA: The New Molecular Markers for Chronic Respiratory Diseases

Idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), asthma and sleep disorders are chronic respiratory diseases that affect the airways, compromising lung function over time. These diseases affect hundreds of millions of people around the world and their frequency seems to be increasing every year. Extracellular vesicles (EVs) are small-sized vesicles released by every cell in the body. They are present in most body fluids and contain various biomolecules including proteins, lipids, mRNA and non-coding RNA (micro-RNA). The EVs can release their cargo, specifically micro-RNAs (miRNAs), to both neighboring and/or distal cells, playing a fundamental role in cell-cell communication. Recent studies have shown their possible role in the pathogenesis of various chronic respiratory diseases. The expression of miRNAs and, in particular, of miRNAs contained within the extracellular vesicles seems to be a good starting point in order to identify new potential biomarkers of disease, allowing a non-invasive clinical diagnosis. In this review we summarize some studies, present in the literature, about the functions of extracellular vesicles and miRNAs contained in extracellular vesicles in chronic respiratory diseases and we discuss the potential clinical applications of EVs and EVs-miRNAs for their possible use such as future biomarkers.

Exosomal Micro-RNAs as Intercellular Communicators in Idiopathic Pulmonary Fibrosis

Communication between neighboring or distant cells is made through a complex network that includes extracellular vesicles (EVs). Exosomes, which are a subgroup of EVs, are released from most cell types and have been found in biological fluids such as urine, plasma, and airway secretions like bronchoalveolar lavage (BAL), nasal lavage, saliva, and sputum. Mainly, the cargo exosomes are enriched with mRNAs and microRNAs (miRNAs), which can be transferred to a recipient cell consequently modifying and redirecting its biological function. The effects of miRNAs derive from their role as gene expression regulators by repressing or degrading their target mRNAs. Nowadays, various types of research are focused on evaluating the potential of exosomal miRNAs as biomarkers for the prognosis and diagnosis of different pathologies. Nevertheless, there are few reports on their role in the pathophysiology of idiopathic pulmonary fibrosis (IPF), a chronic lung disease characterized by progressive lung scarring with no cure. In this review, we focus on the role and effect of exosomal miRNAs as intercellular communicators in the onset and progression of IPF, as well as discussing their potential utility as therapeutic agents for the treatment of this disease.

Role of microRNAs in type 2 diseases and allergen-specific immunotherapy

MicroRNAs (miRs) have gained scientific attention due to their importance in the pathophysiology of allergic diseases as well as their potential as biomarkers in allergen-specific treatment options. Their function as post-transcriptional regulators, controlling various cellular processes, is of high importance since any single miR can target multiple mRNAs, often within the same signalling pathway. MiRs can alter dysregulated expression of certain cellular responses and contribute to or cause, but in some cases prevent or repress, the development of various diseases. In this review article, we describe current research on the role of specific miRs in regulating immune responses in epithelial cells and specialized immune cells in response to various stimuli, in allergic diseases, and regulation in the therapeutic approach of allergen-specific immunotherapy (AIT). Despite the fact that AIT has been used successfully as a causative treatment option since more than a century, very little is known about the mechanisms of regulation and its connections with microRNAs. In order to fill this gap, this review aims to provide an overview of the current knowledge.

Interrelation between extracellular vesicles miRNAs with chronic lung diseases

Extracellular vehicles (EVs) are nanoscale lipid bilayer vesicles that carry biologically active biomolecule cargos like proteins, lipids, and nucleic acids (DNA, RNA) outside of the cell. Blood (serum/plasma), urine, and bronchoalveolar lavage fluid are all examples of biofluids from which they may be collected. EVs play a vital role in intracellular communication. The molecular signature of EVs largely depends on the parental cell's status. EVs are classified into two groups, (1) exosomes (originated by endogenous route) and (2) microvesicles (originated from the plasma membrane, also known as ectosomes). The quantity and types of EV cargo vary during normal conditions compared to pathological conditions (chronic inflammatory lung diseases or lung cancer). Consequently, EVs contain novel biomarkers that differ based on the cell type of origin and during lung diseases. Small RNAs (e.g., microRNAs) are transported by EVs, which is one of the most rapidly evolving research areas in the field of EVs biology. EV-mediated cargos transport small RNAs that can result in reprograming the target/recipient cells. Multiple chronic inflammatory lung illnesses, such as chronic obstructive pulmonary disease, asthma, pulmonary hypertension, pulmonary fibrosis, cystic fibrosis, acute lung injury, and lung cancer, have been demonstrated to be regulated by EV. In this review, we will consolidate the current knowledge and literature on the novel role of EVs and their small RNAs concerning chronic lung diseases (CLDs). Additionally, we will also provide better insight into the clinical and translational impact of mesenchymal stem cells-derived EVs as novel therapeutic agents in treating CLDs.

Detection of Epidermal Growth Factor Receptor Expression in Breast Cancer Cell Lines Using an Ion-Sensitive Field-Effect Transistor in Combination with Enzymatic Chemical Signal Amplification

A novel strategy for epidermal growth factor receptor (EGFR) detection using a cell-based field-effect transistor (FET) with enzymatic chemical signal amplification is proposed. Four human breast cancer cell lines [BT474, MDA-MB-231 (MM231), MDA-MB-468 (MM468), and MDA-MB-453 (MM453)] were used to compare the expression levels of EGFR. The cells were non-specifically captured on the surface of the gate of the FET, irrespective of their surface antigens. With this configuration, the heterogeneity of the cells would be analyzed using secondary antibodies conjugated to different kinds of enzymes. Four breast cancer cell lines with different levels of EGFR expression were captured on the respective surfaces of the extracellular matrix (ECM) gel-coated gates of the FETs. Glucose oxidase (GOx) was conjugated to the secondary antibody, and the output signals of the cell-based FETs changed depending on the expression levels of EGFR upon addition of glucose. The order of the expression levels of EGFR among the four cell lines, determined with the cell-based FETs, was consistent with the results of fluorescence detection determined by fluorescence-activated cell sorting (FACS). The cell-based FETs are advantageous for miniaturization and in massive parallel analyses of target molecules expressed on the membranes of cells and EVs, and their small size and cost effectiveness for cancer testing could enable their realization in a future liquid biopsy.

Role of extracellular vesicles in lung diseases

ABSTRACT

Extracellular vesicles (EVs) are anuclear particles composed of lipid bilayers that contain nucleic acids, proteins, lipids, and organelles. EVs act as an important mediator of cell-to-cell communication by transmitting biological signals or components, including lipids, proteins, messenger RNAs, DNA, microRNAs, organelles, etc, to nearby or distant target cells to activate and regulate the function and phenotype of target cells. Under physiological conditions, EVs play an essential role in maintaining the homeostasis of the pulmonary milieu but they can also be involved in promoting the pathogenesis and progression of various respiratory diseases including chronic obstructive pulmonary disease, asthma, acute lung injury/acute respiratory distress syndrome, idiopathic pulmonary fibrosis (IPF), and pulmonary artery hypertension. In addition, in multiple preclinical studies, EVs derived from mesenchymal stem cells (EVs) have shown promising therapeutic effects on reducing and repairing lung injuries. Furthermore, in recent years, researchers have explored different methods for modifying EVs or enhancing EVs-mediated drug delivery to produce more targeted and beneficial effects. This article will review the characteristics and biogenesis of EVs and their role in lung homeostasis and various acute and chronic lung diseases and the potential therapeutic application of EVs in the field of clinical medicine.

The Interaction Network of MicroRNAs with Cytokines and Signaling Pathways in Allergic Asthma

Allergic asthma is a complicated disease that is affected by many factors. Numerous cytokines and signaling pathways are attributed to the cause of asthma symptoms. MicroRNAs (miRNAs) are a group of small non-coding single-stranded RNA molecules that are involved in gene silencing and posttranscriptional regulation of gene expression by targeting mRNAs. In pathological conditions, altered expression of microRNAs differentially regulates cytokines and signaling pathways and therefore, can be the underlying reason for the pathogenesis of allergic asthma. Indeed, microRNAs participate in airway inflammation via inducing airway structural cells and activating immune responses by targeting cytokines and signaling pathways. Thus, to make a complete understanding of allergic asthma, it is necessary to investigate the communication network of microRNAs with cytokines and signaling pathways which is contributed to the pathogenesis of allergic asthma. Here, we shed light on this aspect of asthma pathology by Summarizing our current knowledge of this topic.

Cucurbitacin E ameliorates airway remodelling by inhibiting nerve growth factor expression in nicotine-treated bronchial epithelial cells and mice: The key role of let-7c-5p up-regulated expression

Cucurbitacin E (CuE) shows potential to handle airway remodelling. In the current study, the effects of CuE on nicotine-induced airway remodelling were explored by focussing on its interaction with let-7c-5p/NGF axis. The potential microRNA (miR) as the therapeutic target for CuE treatment was determined using a microarray assay. Changes in viability, inflammation and let-7c-5p/NGF pathway in nicotine-treated bronchial epithelial cells (BECs) were detected under CuE treatment (5 μM). The pathways were manipulated with let-7c-5p inhibitor. Mice were subjected to nicotine treatment and handled with CuE. Changes in pulmonary function and structure were detected. Based on the microarray data, let-7c-5p was selected as the therapeutic target. Viability and inflammation of BECs were induced by nicotine and then restored by CuE. At molecular level, nicotine suppressed let-7c-5p while induced NGF, FN1 and COLIA levels. The effects of CuE were counteracted by let-7c-5p inhibition. In a mouse model, nicotine impaired the function and structure of lung, which was attenuated by CuE and then re-impaired by let-7c-5p antagomir. Collectively, CuE protected against nicotine-induced airway remodelling and partially depended on the induction of let-7c-5p; our future work would pay more attention to other downstream effectors of the miR to promote the treatment of nicotine-induced pulmonary disorders.

Epigenetic regulation of immune function in asthma

Asthma is a common complex respiratory disease characterized by chronic airway inflammation and partially reversible airflow obstruction resulting from genetic and environmental determinants. Because epigenetic marks influence gene expression and can be modified by both environmental exposures and genetic variation, they are increasingly recognized as relevant to the pathogenesis of asthma and may be a key link between environmental exposures and asthma susceptibility. Unlike changes to DNA sequence, epigenetic signatures are dynamic and reversible, creating an opportunity for not only therapeutic targets but may serve as biomarkers to follow disease course and identify molecular subtypes in heterogeneous diseases such as asthma. In this review, we will examine the relationship between asthma and 3 key epigenetic processes that modify gene expression: DNA methylation, modification of histone tails, and noncoding RNAs. In addition to presenting a comprehensive assessment of the existing epigenetic studies focusing on immune regulation in asthma, we will discuss future directions for epigenetic investigation in allergic airway disease.

Tetraspanins distinguish separate extracellular vesicle subpopulations in human serum and plasma - Contributions of platelet extracellular vesicles in plasma samples

BACKGROUND

The ability to isolate extracellular vesicles (EVs) from blood is vital in the development of EVs as disease biomarkers. Both serum and plasma can be used, but few studies have compared these sources in terms of the type of EVs that are obtained. The aim of this study was to determine the presence of different subpopulations of EVs in plasma and serum.

METHOD

Blood was collected from healthy subjects, and plasma and serum were isolated in parallel. ACD or EDTA tubes were used for the collection of plasma, while serum was obtained in clot activator tubes. EVs were isolated utilising a combination of density cushion and SEC, a combination of density cushion and gradient or by a bead antibody capturing system (anti-CD63, anti-CD9 and anti-CD81 beads). The subpopulations of EVs were analysed by NTA, Western blot, SP-IRIS, conventional and nano flow cytometry, magnetic bead ELISA and mass spectrometry. Additionally, different isolation protocols for plasma were compared to determine the contribution of residual platelets in the analysis.

RESULTS

This study shows that a higher number of CD9+ EVs were present in EDTA-plasma compared to ACD-plasma and to serum, and the presence of CD41a on these EVs suggests that they were released from platelets. Furthermore, only a very small number of EVs in blood were double-positive for CD63 and CD81. The CD63+ EVs were enriched in serum, while CD81+ vesicles were the rarest subpopulation in both plasma and serum. Additionally, EDTA-plasma contained more residual platelets than ACD-plasma and serum, and two centrifugation steps were crucial to reduce the number of platelets in plasma prior to EV isolation.

CONCLUSION

These results show that human blood contains multiple subpopulations of EVs that carry different tetraspanins. Blood sampling methods, including the use of anti-coagulants and choice of centrifugation protocols, can affect EV analyses and should always be reported in detail.

RNA sequencing reveals the emerging role of bronchoalveolar lavage fluid exosome lncRNAs in acute lung injury

Background

Bronchoalveolar lavage fluid (BALF) exosomes possess different properties in different diseases, which are mediated through microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), among others. By sequencing the differentially expressed lncRNAs in BALF exosomes, we seek potential targets for the diagnosis and treatment of acute lung injury (ALI).

Methods

Considering that human and rat genes are about 80% similar, ALI was induced using lipopolysaccharide in six male Wistar rats, with six rats as control (all weighing 200 ± 20 g and aged 6-8 weeks). BALF exosomes were obtained 24 h after ALI. The exosomes in BALF were extracted by ultracentrifugation. The differential expression of BALF exosomal lncRNAs in BALF was analyzed by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the functions of differentially expressed lncRNAs, which were confirmed by reverse transcription-polymerase chain reaction.

Results

Compared with the control group, the ALI group displayed a higher wet/dry ratio, tumor necrosis factor-α levels, and interleukin-6 levels (all P < 0.001). The airway injection of exosomes in rats led to significant infiltration by neutrophils. A total of 2,958 differentially expressed exosomal lncRNAs were identified, including 2,524 upregulated and 434 downregulated ones. Five lncRNAs confirmed the reliability of the sequencing data. The top three GO functions were phagocytic vesicle membrane, regulation of receptor biosynthesis process, and I-SMAD binding. Salmonella infection, Toll-like receptor signaling pathway, and osteoclast differentiation were the most enriched KEGG pathways. The lncRNA-miRNA interaction network of the five confirmed lncRNAs could be predicted using miRDB.

Conclusions

BALF-derived exosomes play an important role in ALI development and help identify potential therapeutic targets related to ALI.

MicroRNAs: A Promising Tool for Asthma Diagnosis and Severity Assessment. A Systematic Review

Micro RNAs (miRNAs) are short, non-coding RNAs (Ribonucleic acids) with regulatory functions that could prove useful as biomarkers for asthma diagnosis and asthma severity-risk stratification. The objective of this systematic review is to identify panels of miRNAs that can be used to support asthma diagnosis and severity-risk assessment. Three databases (Medline, Embase, and SCOPUS) were searched up to 15 September 2020 to identify studies reporting differential expression of specific miRNAs in the tissues of adults and children with asthma. Studies reporting miRNAs associations in animal models that were also studied in humans were included in this review. We identified 75 studies that met our search criteria. Of these, 66 studies reported more than 200 miRNAs that are differentially expressed in asthma patients when compared to non-asthmatic controls. In addition, 16 studies reported 17 miRNAs that are differentially expressed with differences in asthma severity. We were able to construct two panels of miRNAs that are expressed in blood and can serve as core panels to further investigate the practicality and efficiency of using miRNAs as non-invasive biomarkers for asthma diagnosis and severity-risk assessment, respectively.

Side-Directed Release of Differential Extracellular Vesicle-associated microRNA Profiles from Bronchial Epithelial Cells of Healthy and Asthmatic Subjects

Extracellular vesicles (EVs) are released by virtually all cells and may serve as intercellular communication structures by transmitting molecules such as proteins, lipids, and nucleic acids between cells. MicroRNAs (miRNAs) are an abundant class of vesicular RNA playing a pivotal role in regulating intracellular processes. In this work, we aimed to characterize vesicular miRNA profiles released in a side-directed manner by bronchial epithelial cells from healthy and asthmatic subjects using an air−liquid interface cell culture model. EVs were isolated from a culture medium collected from either the basolateral or apical cell side of the epithelial cell cultures and characterized by nano-flow cytometry (NanoFCM) and bead-based flow cytometry. EV-associated RNA profiles were assessed by small RNA sequencing and subsequent bioinformatic analyses. Furthermore, miRNA-associated functions and targets were predicted and miRNA network analyses were performed. EVs were released at higher numbers to the apical cell side of the epithelial cells and were considerably smaller in the apical compared to the basolateral compartment. EVs from both compartments showed a differential tetraspanins surface marker expression. Furthermore, 236 miRNAs were differentially expressed depending on the EV secretion side, regardless of the disease phenotype. On the apical cell side, 32 miRNAs were significantly altered in asthmatic versus healthy conditions, while on the basolateral cell side, 23 differentially expressed miRNAs could be detected. Downstream KEGG pathway analysis predicted mTOR and MAPK signaling pathways as potential downstream targets of apically secreted miRNAs. In contrast, miRNAs specifically detected at the basolateral side were associated with processes of T and B cell receptor signaling. The study proves a compartmentalized packaging of EVs by bronchial epithelial cells supposedly associated with site-specific functions of cargo miRNAs, which are considerably affected by disease conditions such as asthma.

The Potential of Exosomes in Allergy Immunotherapy

Allergic diseases represent a global health and economic burden of increasing significance. The lack of disease-modifying therapies besides specific allergen immunotherapy (AIT) which is not available for all types of allergies, necessitates the study of novel therapeutic approaches. Exosomes are small endosome-derived vesicles delivering cargo between cells and thus allowing inter-cellular communication. Since immune cells make use of exosomes to boost, deviate, or suppress immune responses, exosomes are intriguing candidates for immunotherapy. Here, we review the role of exosomes in allergic sensitization and inflammation, and we discuss the mechanisms by which exosomes could potentially be used in immunotherapeutic approaches for the treatment of allergic diseases. We propose the following approaches: (a) Mast cell-derived exosomes expressing IgE receptor FcεRI could absorb IgE and down-regulate systemic IgE levels. (b) Tolerogenic exosomes could suppress allergic immune responses via induction of regulatory T cells. (c) Exosomes could promote TH1-like responses towards an allergen. (d) Exosomes could modulate IgE-facilitated antigen presentation.

Adipose-Derived Mesenchymal Stem Cell-Derived Exosomal miR-301a-3p Regulates Airway Smooth Muscle Cells During Asthma by Targeting STAT3

Background

Asthma is a chronic inflammatory disease featured by inflammation and remodeling of airway. Adipose-derived mesenchymal stem cell (ADSCs)-derived exosomal miRNAs have been suggested as promising therapeutic manners for diseases.

Methods

ADSCs and airway smooth muscle cells (ASMCs) were isolated from SD rats. Flow cytometry was conducted to detect the surface biomarkers of isolated cells. Exosomes were extracted by sequentially centrifuge method and identified by Western blotting and nanoparticle tracking analysis (NTA). Uptake of exosomes by ASMCs was detected by confocal assay. ASMCs were treated with platelet-derived growth factor-BB (PDGF-BB) to mimic cell remodeling and inflammation. Cell counting 8 (CCK-8), Transwell, and flow cytometry were performed to determine the viability, migration, and apoptosis of ASMCs. Release of inflammatory factors was detected by enzyme-linked immunosorbent assay (ELISA). Levels of RNAs and proteins were measured by quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay. Interaction between miR-301a-3p and signal transducer and activator of transcription 3 (STAT3) was determined by luciferase reporter gene assay. The effect of Exosomal miR-301a-3p was analyzed in ovalbumin (OVA)-induced asthma mouse model.

Results

ADSCs-derived exosomes could be effectively internalized by ASMCs. Exosomal miR-301a-3p notably suppressed the PDGF-BB-stimulated proliferation and migration of ASMCs, and enhanced apoptosis, as well as decreased the secretion of inflammatory factors. MiR-301a-3p directly targeted the 3ʹUTR region of STAT3. STAT3 overexpression reversed the suppressive effects of exosomal miR-301a-3p on ASMCs under PDGF-BB stimulation. The expression of miR-301a-3p and STAT3 was negative correlation in specimen from patients with asthma. Exosomal miR-301a-3p inhibited OVA-induced lung injury by targeting STAT3 in mice.

Conclusion

This study exposed that exosomal miR-301a-3p from ADSCs could effectively alleviate PDGF-BB-stimulated remodeling and inflammation of ASMCs via targeting STAT3, presented ADSCs-derived exosomal miR-301a-3p as a promising therapeutic approach for asthma.

Gene network analysis for identification of microRNA biomarkers for asthma

BACKGROUND

To date, reliable biomarkers for asthma have not been identified. MicroRNAs (miRNAs) are small, non-coding RNAs that negatively regulate post-transcriptional gene expression, and they are involved in various diseases, including asthma. MiRNAs may serve as ideal biomarkers due to their ability to regulate multiple pathways. This study aims to identify miRNA biomarker signatures for asthma.

METHODS

We used the house dust mite (HDM) mouse model of allergic inflammation. Mice were phenotyped by assessing lung function, allergic response, airway inflammation, and remodeling. The miRNA signature profiles in serum and lung tissue were determined by small RNA sequencing, and data were analyzed using Qiagen CLC Genomics Workbench. To identify relevant gene targets, we performed mRNA sequencing, followed by miRNA-targets analysis. These miRNAs and targets were subject to subsequent pathway and functional analyses.

RESULTS

Mice exposed to HDM developed phenotypic features of allergic asthma. miRNA sequencing analysis showed that 213 miRNAs were substantially dysregulated (FDR p-value < 0.05 and fold change expression >  + 1.5 and < - 1.5) in the lung of HDM mice relative to the control mice. In contrast, only one miRNA (miR-146b-5p) was significantly increased in serum. Target analysis of lung dysregulated miRNAs revealed a total of 131 miRNAs targeting 211 mRNAs. Pathway analysis showed T helper 2/1 (Th2/Th1) as the top significantly activated signaling pathway associated with the dysregulated miRNAs. The top enriched diseases were inflammatory response and disease, which included asthma. Asthma network analysis indicated that 113 of 131 miRNAs were directly associated with asthma pathogenesis.

CONCLUSIONS

These findings suggest that most dysregulated miRNAs in the HDM model were associated with asthma pathogenesis via Th2 signaling. We identified a panel of 30 miRNAs as potential biomarker candidates for asthma.