Biomarkers and asthma management: analysis and potential applications

In-silico identification and prioritization of therapeutic targets of asthma

Asthma is a "common chronic disorder that affects the lungs causing variable and recurring symptoms like repeated episodes of wheezing, breathlessness, chest tightness and underlying inflammation. The interaction of these features of asthma determines the clinical manifestations and severity of asthma and the response to treatment" [cited from: National Heart, Lung, and Blood Institute. Expert Panel 3 Report. Guidelines for the Diagnosis and Management of Asthma 2007 (EPR-3). Available at: https://www.ncbi.nlm.nih.gov/books/NBK7232/ (accessed on January 3, 2023)]. As per the WHO, 262 million people were affected by asthma in 2019 that leads to 455,000 deaths ( https://www.who.int/news-room/fact-sheets/detail/asthma ). In this current study, our aim was to evaluate thousands of scientific documents and asthma associated omics datasets to identify the most crucial therapeutic target for experimental validation. We leveraged the proprietary tool Ontosight® Discover to annotate asthma associated genes and proteins. Additionally, we also collected and evaluated asthma related patient datasets through bioinformatics and machine learning based approaches to identify most suitable targets. Identified targets were further evaluated based on the various biological parameters to scrutinize their candidature for the ideal therapeutic target. We identified 7237 molecular targets from published scientific documents, 2932 targets from genomic structured databases and 7690 dysregulated genes from the transcriptomics and 560 targets from genomics mutational analysis. In total, 18,419 targets from all the desperate sources were analyzed and evaluated though our approach to identify most promising targets in asthma. Our study revealed IL-13 as one of the most important targets for asthma with approved drugs on the market currently. TNF, VEGFA and IL-18 were the other top targets identified to be explored for therapeutic benefit in asthma but need further clinical testing. HMOX1, ITGAM, DDX58, SFTPD and ADAM17 were the top novel targets identified for asthma which needs to be validated experimentally.

Severe Acute Bronchial Asthma with Sepsis: Determining the Status of Biomarkers in the Diagnosis of the Disease

Bronchial asthma is a widely prevalent illness that substantially impacts an individual's health standard worldwide and has a significant financial impact on society. Global guidelines for managing asthma do not recommend the routine use of antimicrobial agents because most episodes of the condition are linked to viral respiratory tract infections (RTI), and bacterial infection appears to have an insignificant impact. However, antibiotics are recommended when there is a high-grade fever, a consolidation on the chest radiograph, and purulent sputum that contains polymorphs rather than eosinophils. Managing acute bronchial asthma with sepsis, specifically the choice of whether or not to initiate antimicrobial treatment, remains difficult since there are currently no practical clinical or radiological markers that allow for a simple distinction between viral and bacterial infections. Researchers found that serum procalcitonin (PCT) values can efficiently and safely minimize antibiotic usage in individuals with severe acute asthma. Again, the clinical manifestations of acute asthma and bacterial RTI are similar, as are frequently used test values, like C-reactive protein (CRP) and white blood cell (WBC) count, making it harder for doctors to differentiate between viral and bacterial infections in asthma patients. The role and scope of each biomarker have not been precisely defined yet, although they have all been established to aid healthcare professionals in their diagnostics and treatment strategies.

THE LEVEL OF REACTIVE OXYGEN SPECIES AS A MARKER OF ASTHMA SEVERITY IN CHILDREN

OBJECTIVE

The aim of the research was to assess the reactive oxygen species (ROS) levels in granulocytes of patients with asthma.

PATIENTS AND METHODS

Materials and methods: The study involved 35 children aged 5 to 17 years. 26 children with persistent asthma, partially controlled course in the period of exacerbation were divided into groups: 1 group - mild asthma (n = 12), group 2 - moderate asthma (n = 7) group 3 - severe asthma (n = 7) and control group included almost healthy children (n = 9). ROS levels in granulocytes were evaluated using BD FACSDiva™. The spirographic complex was used to assess the function of external respiration.

RESULTS

Results: The level of ROS in granulocytes of patients with severe asthma was significantly reduced compared with children in the control group and patients with mild and moderate asthma (p₁-₃ = 0.0003, p₂-₃ = 0.0017, p c-₃ = 0.0150). The concentration of ROS in granulocytes ≤ 285 a.u. was prognostically significant with high specificity and sensitivity with severe asthma.

CONCLUSION

Conclusions: The concentration of ROS levels in neutrophils in patients with severe asthma probably reflected the suppression of their products, which suggests the depletion of the reserve capacity of neutrophils. Decreased concentrations of reactive oxygen species in children with asthma can be considered as a possible marker of asthma severity.

Precision Medicine in Asthma Therapy

Asthma is a complex, heterogeneous disease that necessitates a proper patient evaluation to decide the correct treatment and optimize disease control. The recent introduction of new target therapies for the most severe form of the disease has heralded a new era of treatment options, intending to treat and control specific molecular pathways in asthma pathophysiology. Precision medicine, using omics sciences, investigates biological and molecular mechanisms to find novel biomarkers that can be used to guide treatment selection and predict response. The identification of reliable biomarkers indicative of the pathological mechanisms in asthma is essential to unravel new potential treatment targets. In this chapter, we provide a general description of the currently available -omics techniques, focusing on their implications in asthma therapy.

The potential role of SP-D as an early biomarker of severity of asthma

Surfactant decreases the surface tension of peripheral airways and modulates the immunological responses of the lung. The alterations of surfactant due to the airway inflammation suggest a role in the pathogenesis of asthma. We aim to test the hypothesis that serum levels of SP-A (Surfactant Protein A) and SP-D (Surfactant Protein-D) are altered in patients with mild asthma compared to healthy controls and those alterations are related to functional abnormalities of peripheral airways, which are an early marker of progression of asthma. In this pilot study, we recruited 20 mild asthmatics and 10 healthy controls. We measured serum SP-A and SP-D and all subjects underwent clinical, lung functional and biological assessments. Serum SP-D was significantly higher in asthmatics compared to healthy controls (mean (SD) values: 7.9(4.65) vs 3.31(1.71) ng ml^-1,p-value: 0.008). In the asthmatic group, serum SP-D was significantly correlated to CalvNO (alveolar NO concentration) (R-squared: 0.26;p-value: 0.014). These preliminary findings suggest that serum SP-D could be used as a lung-specific biomarker of small airways damage thus predicting the progression to the most severe forms of asthma.

Milestones of Precision Medicine: An Innovative, Multidisciplinary Overview

Although the concept of precision medicine, in which healthcare is tailored to the molecular and clinical characteristics of each individual, is not new, its implementation in clinical practice has been heterogenous. In some medical specialties, precision medicine has gone from being just a promise to a reality that achieves better patient outcomes. This is a fact if we consider, for example, the great advances made in the genetic diagnosis and subsequent treatment of countless hereditary diseases, such as cystic fibrosis, which have improved the life expectancy of many of the affected children. In the field of oncology, the development of targeted therapies has prolonged the survival of patients with breast, lung, colorectal, melanoma, and hematological malignancies. In other disciplines, clinical milestones are perhaps less well known, but no less important. The current challenge is to expand and generalize the use of technologies that are central to precision medicine, such as massively parallel sequencing, to improve the management (prevention and treatment) of complex conditions such as cardiovascular, kidney, or autoimmune diseases. This process requires investment in specialized expertise, multidisciplinary collaboration, and the nationwide organization of genetic laboratories for diagnosis of specific diseases.

Nasal DNA methylation differentiates severe from non-severe asthma in African-American children

BACKGROUND

Asthma is highly heterogeneous, and severity evaluation is key to asthma management. DNA methylation (DNAm) contributes to asthma pathogenesis. This study aimed to identify nasal epithelial DNAm differences between severe and nonsevere asthmatic children and evaluate the impact of environmental exposures.

METHODS

Thirty-three nonsevere and 22 severe asthmatic African American children were included in an epigenome-wide association study. Genome-wide nasal epithelial DNAm and gene expression were measured. CpG sites associated with asthma severity and environmental exposures and predictive of severe asthma were identified. DNAm was correlated with gene expression. Enrichment for transcription factor (TF) binding sites or histone modifications surrounding DNAm differences were determined.

RESULTS

We identified 816 differentially methylated CpG positions (DMPs) and 10 differentially methylated regions (DMRs) associated with asthma severity. Three DMPs exhibited discriminatory ability for severe asthma. Intriguingly, six DMPs were simultaneously associated with asthma, allergic asthma, total IgE, environmental IgE, and FeNO in an independent cohort of children. Twenty-seven DMPs were associated with traffic-related air pollution or secondhand smoke. DNAm at 22 DMPs was altered by diesel particles or allergen in human bronchial epithelial cells. DNAm levels at 39 DMPs were correlated with mRNA expression. Proximal to 816 DMPs, three histone marks and several TFs involved in asthma pathogenesis were enriched.

CONCLUSIONS

Significant differences in nasal epithelial DNAm were observed between nonsevere and severe asthma in African American children, a subset of which may be useful to predict disease severity. These CpG sites are subjected to the influences of environmental exposures and may regulate gene expression.

Prioritizing Molecular Biomarkers in Asthma and Respiratory Allergy Using Systems Biology

Highly prevalent respiratory diseases such as asthma and allergy remain a pressing health challenge. Currently, there is an unmet need for precise diagnostic tools capable of predicting the great heterogeneity of these illnesses. In a previous study of 94 asthma/respiratory allergy biomarker candidates, we defined a group of potential biomarkers to distinguish clinical phenotypes (i.e. nonallergic asthma, allergic asthma, respiratory allergy without asthma) and disease severity. Here, we analyze our experimental results using complex algorithmic approaches that establish holistic disease models (systems biology), combining these insights with information available in specialized databases developed worldwide. With this approach, we aim to prioritize the most relevant biomarkers according to their specificity and mechanistic implication with molecular motifs of the diseases. The Therapeutic Performance Mapping System (Anaxomics’ TPMS technology) was used to generate one mathematical model per disease: allergic asthma (AA), non-allergic asthma (NA), and respiratory allergy (RA), defining specific molecular motifs for each. The relationship of our molecular biomarker candidates and each disease was analyzed by artificial neural networks (ANNs) scores. These analyses prioritized molecular biomarkers specific to the diseases and to particular molecular motifs. As a first step, molecular characterization of the pathophysiological processes of AA defined 16 molecular motifs: 2 specific for AA, 2 shared with RA, and 12 shared with NA. Mechanistic analysis showed 17 proteins that were strongly related to AA. Eleven proteins were associated with RA and 16 proteins with NA. Specificity analysis showed that 12 proteins were specific to AA, 7 were specific to RA, and 2 to NA. Finally, a triggering analysis revealed a relevant role for AKT1, STAT1, and MAPK13 in all three conditions and for TLR4 in asthmatic diseases (AA and NA). In conclusion, this study has enabled us to prioritize biomarkers depending on the functionality associated with each disease and with specific molecular motifs, which could improve the definition and usefulness of new molecular biomarkers.

Bronchiectasis in Severe Asthma: Does It Make a Difference?

BACKGROUND

Asthma and bronchiectasis are 2 heterogeneous diseases that frequently coexist, particularly in severe asthma. Recognition of this co-diagnosis may importantly affect treatment decisions and outcome. Previous studies in asthma with bronchiectasis show inconsistent outcomes, probably due to the heterogeneity of the included asthma cohorts.

OBJECTIVES

We hypothesized that bronchiectasis contributes to asthma severity and that patients with severe asthma and bronchiectasis present with distinct characteristics resulting in different treatable traits. In addition, we explored whether bronchiectasis in severe asthma is more common in a specific phenotype.

METHODS

This is a single-center study consecutively including patients with severe asthma from a tertiary referral center. Severe asthma was diagnosed according to the ATS/ERS guidelines. Asthma and infectious exacerbations were defined by the attending specialist as respiratory symptoms requiring treatment with systemic steroids or antibiotics, respectively. Two independent blinded radiologists evaluated each CT.

RESULTS

19% of patients with severe asthma showed bronchiectasis on CT. Patients with bronchiectasis had a lower FEV1% predicted (p = 0.02) and FEV1/FVC (p = 0.004) and more infectious exacerbations (p = 0.003) compared to patients without bronchiectasis. Bronchiectasis is more common in patients with a longer duration of asthma, sensitization to A. fumigatus or a positive sputum culture. Sputum cultures of patients with severe asthma and bronchiectasis revealed more P. aeruginosa, S. maltophilia, H. parainfluenzae, and A. fumigates compared to the non-bronchiectasis group. The adult-onset, eosinophilic asthma phenotype showed the highest prevalence of bronchiectasis (29.4%).

CONCLUSIONS

Patients with severe asthma and coexisting bronchiectasis were found to represent a distinct group, in terms of disease severity, microbiology, and asthma phenotype. Performing (HR)CT and sputum cultures can help to identify these patients. These results can possibly contribute to early recognition and targeted treatment of this patient group.

Minimal clinically important difference for asthma endpoints: an expert consensus report

Minimal clinically important difference (MCID) can be defined as the smallest change or difference in an outcome measure that is perceived as beneficial and would lead to a change in the patient's medical management.

The aim of the current expert consensus report is to provide a “state-of-the-art” review of the currently available literature evidence about MCID for end-points to monitor asthma control, in order to facilitate optimal disease management and identify unmet needs in the field to guide future research.

A series of MCID cut-offs are currently available in literature and validated among populations of asthmatic patients, with most of the evidence focusing on outcomes as patient reported outcomes, lung function and exercise tolerance. On the contrary, only scant and partial data are available for inflammatory biomarkers. These clearly represent the most interesting target for future development in diagnosis and clinical management of asthma, particularly in view of the several biologic drugs in the pipeline, for which regulatory agencies will soon require personalised proof of efficacy and treatment response predictors.

Minimal clinically important difference (MCID) cut-offs in asthma are validated for patient reported outcomes and lung function, but not for inflammatory biomarkers. MCID represents a key target for future development in asthma management. http://bit.ly/33hcWIe

Evaluation serum levels of YKL-40, Periostin, and some inflammatory cytokines together with IL-37, a new anti-inflammatory cytokine, in patients with stable and exacerbated asthma

INTRODUCTION

As asthma has a wide range of inflammatory pathways, the researchers were focused on the markers that may be associated with exacerbation and stability in asthma.

OBJECTIVE

Our aim is to investigate the serum levels of some inflammatory markers and cytokines in stable and exacerbated asthmatic patients.

METHODS

The study included in 59 non-smoker asthma patient (Exacerbated=25, Stable=34) and 30 healthy volunteers. The serum level of periostin, YKL-40, IL-4, IL-5, IL-37, and TNF-α were detected by enzyme-linked immunosorbent assay.

RESULTS

Except for IL-37, the periostin, YKL-40, IL-4, IL-5, and TNF-α level in asthmatic patients were significantly higher than those of healthy control. In the exacerbated group, the periostin, YKL-40, IL-5, and TNF-α level were significantly higher than stable asthma and healthy control groups. The serum levels of IL-4 in exacerbated and stable asthma groups were significantly higher than healthy control group. There was a significant difference between IL4 levels, in stable asthma and healthy control groups. In exacerbated asthma group, IL-37 level was significantly lower than stable and healthy control groups. The highest area under the ROC curve (AUC) was found for IL-4. While there was a significant negative correlation between these parameters and FEV1, there was a positive correlation between IL-37 and FEV1, but not significant.

CONCLUSIONS

This study showed that increased serum periostin, YKL-40, IL-5, IL-4, and TNF-α and decreased serum IL-37 were associated with exacerbation showing uncontrolled asthma.

Resolving Clinical Phenotypes into Endotypes in Allergy: Molecular and Omics Approaches

Allergic diseases are highly complex with respect to pathogenesis, inflammation, and response to treatment. Current efforts for allergic disease diagnosis have focused on clinical evidence as a binary outcome. Although outcome status based on clinical phenotypes (observable characteristics) is convenient and inexpensive to measure in large studies, it does not adequately provide insight into the complex molecular determinants of allergic disease. Individuals with similar clinical diagnoses do not necessarily have similar disease etiologies, natural histories, or responses to treatment. This heterogeneity contributes to the ineffective response to treatment leading to an annual estimated cost of $350 billion in the USA alone. There has been a recent focus to deconvolute the clinical heterogeneity of allergic diseases into specific endotypes using molecular and omics approaches. Endotypes are a means to classify patients based on the underlying pathophysiological mechanisms involving distinct functions or treatment response. The advent of high-throughput molecular omics, immunophenotyping, and bioinformatics methods including machine learning algorithms is facilitating the development of endotype-based diagnosis. As we move to the next decade, we should truly start treating clinical endotypes not clinical phenotype. This review highlights current efforts taking place to improve allergic disease endotyping via molecular omics profiling, immunophenotyping, and machine learning approaches in the context of precision diagnostics in allergic diseases. Graphical Abstract.

Use of Natural Products in Asthma Treatment

Asthma, a disease classified as a chronic inflammatory disorder induced by airway inflammation, is triggered by a genetic predisposition or antigen sensitization. Drugs currently used as therapies present disadvantages such as high cost and side effects, which compromise the treatment compliance. Alternatively, traditional medicine has reported the use of natural products as alternative or complementary treatment. The aim of this review was to summarize the knowledge reported in the literature about the use of natural products for asthma treatment. The search strategy included scientific studies published between January 2006 and December 2017, using the keywords "asthma," "treatment," and "natural products." The inclusion criteria were as follows: (i) studies that aimed at elucidating the antiasthmatic activity of natural-based compounds or extracts using laboratory experiments (in vitro and/or in vivo); and (ii) studies that suggested the use of natural products in asthma treatment by elucidation of its chemical composition. Studies that (i) did not report experimental data and (ii) manuscripts in languages other than English were excluded. Based on the findings from the literature search, aspects related to asthma physiopathology, epidemiology, and conventional treatment were discussed. Then, several studies reporting the effectiveness of natural products in the asthma treatment were presented, highlighting plants as the main source. Moreover, natural products from animals and microorganisms were also discussed and their high potential in the antiasthmatic therapy was emphasized. This review highlighted the importance of natural products as an alternative and/or complementary treatment source for asthma treatment, since they present reduced side effects and comparable effectiveness as the drugs currently used on treatment protocols.

Toward clinically applicable biomarkers for asthma: An EAACI position paper

Inflammation, structural, and functional abnormalities within the airways are key features of asthma. Although these processes are well documented, their expression varies across the heterogeneous spectrum of asthma. Type 2 inflammatory responses are characterized by increased levels of eosinophils, FeNO, and type 2 cytokines in blood and/or airways. Presently, type 2 asthma is the best-defined endotype, typically found in patients with allergic asthma, but surprisingly also in nonallergic patients with (severe) asthma. The etiology of asthma with non-type 2 inflammation is less clear. During the past decade, targeted therapies, including biologicals and small molecules, have been increasingly integrated into treatment strategies of severe asthma. These treatments block specific inflammatory pathways or single mediators. Single or composite biomarkers help to identify patients who will benefit from these treatments. So far, only a few inflammatory biomarkers have been validated for clinical application. The European Academy of Allergy & Clinical Immunology Task Force on Biomarkers in Asthma was initiated to review different biomarker sampling methods and to investigate clinical applicability of new and existing inflammatory biomarkers (point-of-care) to support diagnosis, targeted treatment, and monitoring of severe asthma. Subsequently, we discuss existing and novel targeted therapies for asthma as well as applicable biomarkers.

Discriminatory Molecular Biomarkers of Allergic and Nonallergic Asthma and Its Severity

Asthma is a complex disease comprising various phenotypes and endotypes, all of which still need solid biomarkers for accurate classification. In a previous study, we defined specific genes related to asthma and respiratory allergy by studying the expression of 94 genes in a population composed of 4 groups of subjects: healthy control, nonallergic asthmatic, asthmatic allergic, and nonasthmatic allergic patients. An analysis of differential gene expression between controls and patients revealed a set of statistically relevant genes mainly associated with disease severity, i.e., CHI3L1, IL-8, IL-10, MSR1, PHLDA1, PI3, and SERPINB2. Here, we analyzed whether these genes and their proteins could be potential asthma biomarkers to distinguish between nonallergic asthmatic and asthmatic allergic subjects. Protein quantification was determined by ELISA (in serum) or Western blot (in protein extracted from peripheral blood mononuclear cells or PBMCs). Statistical analyses were performed by unpaired t-test using the Graph-Pad program. The sensitivity and specificity of the gene and protein expression of several candidate biomarkers in differentiating the two groups (and the severity subgroups) was performed by receiver operating characteristic (ROC) curve analysis using the R program. The ROC curve analysis determined single genes with good sensitivity and specificity for discriminating some of the phenotypes. However, interesting combinations of two or three protein biomarkers were found to distinguish the asthma disease and disease severity between the different phenotypes of this pathology using reproducible techniques in easy-to-obtain samples. Gene and protein panels formed by single biomarkers and biomarker combinations have been defined in easily obtainable samples and by standardized techniques. These panels could be useful for characterizing phenotypes of asthma, specifically when differentiating asthma severity.

Serum periostin levels and severity of fibrous dysplasia of bone

Fibrous dysplasia of bone (FD) is a rare congenital bone disease, characterized by a fibrous component in the bone marrow. Periostin has been extensively researched because of its implication in various fibrotic or inflammatory diseases. Periostin may be associated with the burden or the severity of FD. The case control PERIOSDYS study aimed at assessing serum periostin levels in FD patients. Sixty four patients with monostotic or polyostotic disease were included, in order to evaluate whether the concentrations were greater in patients than in 128 healthy age, BMI and sex-matched controls and if they were more elevated in patients with the more severe phenotypes. We found that periostin levels were greater in patients with FD compared to controls (mean = 1085 vs 958 pmol/l, p = 0.026), especially in those with a history of fracture (mean = 1475 vs 966 pmol/l, p = 0.0005), polyostotic forms (mean = 1214 vs 955 pmol/l, p = 0.004) or McCune-Albright syndrome (mean = 1585 vs 1023 pmol/l, p = 0.0048). In contrast, high pain levels were not associated with periostin levels (mean = 1137 vs 1036 pmol/l, p = 0.445). Furthermore, patients undergoing bisphosphonate therapy had significantly lower levels than treatment naïve patients (mean = 953 vs 1370 pmol/l, p = 0.002). In conclusion, periostin may be a biochemical marker indicative of the most severe forms of FD and could be used to monitor patients treated with bisphosphonates.

Impact of reslizumab on outcomes of severe asthmatic patients: current perspectives

Approximately 5%–10% of asthmatics suffer from severe asthma. New biological treatments represent a great opportunity to reduce asthma burden and to improve asthma patients’ lives. Reslizumab will soon be available in several European countries. This anti-IL-5 IgG4/κ monoclonal antibody, administered intravenously at a dose of 3 mg/kg over 20–50 minutes every 4 weeks, has been shown to be safe and effective in patients with 400 eosinophils/μL or more in their peripheral blood. The clinical effects in reducing asthma exacerbations and in improving the quality of life and lung function are clear, but further research is needed to determine the best biological compound for a specific cluster of patients. Research data have shown that in patients who were expressing other clinical features of eosinophilic inflammation over asthma (rhinosinusitis and nasal polyposis), the clinical benefit of reslizumab was greater. Furthermore, it has also been observed that in patients with unsatisfactory response to mepolizumab, reslizumab is able to significantly improve the clinical and biological parameters. The aim of personalized medicine is to provide the right drug to the right patient at the right dose at the right moment. The biological treatments that were developed to modify specific pathological pathways not only provide us with the tools for the management of asthma patients but also clarify the biological mechanisms involved in its pathogenesis.