Introduction
Currently, there are approximately 300 million patients with asthma worldwide [
35]. As a diffuse respiratory disease, the main pathological features of asthma include airway inflammation and remodeling, which result in airflow limitation and bronchial hyperresponsiveness [
17]. Standard inhalation therapy is an effective means of controlling the condition of most asthmatic patients. However, approximately 10% of the patients with asthma do not benefit from such therapies [
13,
28]. Patients with asthma who require high-dose inhaled corticosteroid treatments and a second controller to prevent uncontrolled asthma attacks or who remain uncontrolled despite these treatments are considered to have severe asthma [
38]. The Global Initiative for Asthma (GINA) recommends the corticosteroid, azithromycin, anti-IL4R, anti-thymic stromal lymphopoietin, long-acting muscarine anticholinergic, short-acting β-agonists, and anti-IgE antibody omalizumab for the treatment of severe asthma [
31]. However, as a heterogeneous disease, severe asthma requires complex treatments [
14].
Epigenetics refers to those modifications that alter chromatin and regulate gene expression without altering the underlying DNA sequence [
4]. Chromatin regulators (CRs) are important factors in epigenetics; they are mainly involved in DNA methylation, histone modification, chromatin remodeling, and the production of miRNAs that affect protein concentrations in the cell [
1]. Defective chromatin regulation is associated with the development of multiple diseases [
11]. Corticosteroids have been among the main modalities for the treatment of asthma, but possible reasons for their inefficacy in severe asthma are the failure to recruit HDAC2/SIRT1 and the presence of oxidatively/post-translationally modified HDAC2/SIRT1 in asthmatics [
29]. Epigenetic markers regulate many processes in T lymphocytes in asthma. Furthermore, the identification of DNA methylation of specific nucleotides as biomarkers of asthma has been previously reported [
44]. However, an in-depth study on the role of CRs in severe asthma is important for the treatment and prognosis of this condition.
In this study, we analyzed previously determined gene expression and clinical data of patients with severe asthma and healthy individuals. We also sorted the genes encoding CRs based on information from previous literature. The comprehensive analysis of the data was expected to provide new insights into the treatment and prognosis of severe asthma.
Discussion
Approximately 10% of individuals with asthma are classified as having severe asthma. People with severe asthma not only have a heavy psychological and financial burden but also a high mortality rate [
38]. Defects in chromatin regulation are involved in the development of various diseases [
9]. To investigate the role of CRs in severe asthma, we screened for CRs that were differentially expressed between patients with severe asthma and healthy individuals. These CRs were subjected to enrichment and immunological analyses. A risk score was also constructed to assess the association between CRs and prognosis in patients with severe asthma.
The 80 differentially expressed CRs were mainly enriched in histone modification, chromatin organization, transcription regulator complex, transcription coregulator activity, lysine degradation, and cell cycle. Specialized histone modifications, as the core of chromatin control, can be removed, adjusted, or added to histone units [
18]. It is known that, under specific conditions, naive CD4 + T cells are atypically activated, thus, they differentiate into a Th subpopulation cell type that drives the disease; this is a typical feature of asthma. Moreover, histone modification regulates cell lineage commitment in T cells [
41], and different subtypes of T cells influence immune responses in asthma [
39]. In addition, the Th17 cell lineage is subject to epigenetic plasticity through the remodeling of its chromatin structure [
27]. A study found that genes associated with lysine levels may be also linked to reduced inflammation and the degradation of air pollutants, and that these genes are less abundant in asthmatics [
21]. Furthermore, there are differences in serum metabolites between children with exacerbation-prone and non-exacerbation-prone asthma, with significant differences in those from the lysine pathway [
7].
B cells are a major component of the adaptive immune response to house dust mite allergens. Depletion of B cells in house dust mite-sensitive mice prior to house dust mite stimulation results in decreased allergic responses [
40]. Mast cells also play a role in asthma by secreting mediators with pro-inflammatory and airway constrictive effects, such as histamine and bioactive lipids [
24]. However, the role of NK cells in patients with asthma remains controversial. Studies have reported that NK cells can promote the regression of inflammation by inducing eosinophil apoptosis [
6]. Impaired cytotoxicity of peripheral blood NK cells has also been found in patients with severe asthma, suggesting an impaired ability to manage severe asthmatic inflammation [
3,
10]. This study revealed differences in multiple immune cells between patients with severe asthma and healthy individuals.
To further investigate the relationship between CRs and prognosis in patients with severe asthma, we constructed a prognostic prediction model using the four identified key CRs:
SMARCC1,
CHD8,
SETD2, and
KMT2B. The model showed a good predictive performance for prognosis. It is known that the association of the SWI/SNF chromatin remodeling complex with cell cycle checkpoint genes controls cell proliferation and that SMARCC1 is an important member of the SWI/SNF complex; SMARCC1 also plays an important role in development [
8]. The SWI/SNF complex has been observed in chronic rhinosinusitis, and it is possibly involved in the pathophysiology of the disease [
19]. Patients with high blood eosinophil counts had lower levels of expression of the BAF155 protein, whereas patients with high histopathological eosinophil counts had lower expression of all SWI/SNF subunits [
19].
SETD2 is a histone modifier responsible for the trimethylation of lysine 36 of histone H3 (H3K36) [
22]. Air pollution has been linked to several lung diseases, and particulate matter of 10 μm in diameter (PM10) induces aneuploidy and leads to the generation of chromosomal instability in A549 cells by downregulating SETD2 [
33]. Our model also involved
KMT2B, which encodes an enzyme involved in histone H3 lysine 4 (H3K4) methylation [
26], and
CHD8, which encodes for a member of the chromodomain-helicase-DNA binding protein family that has been reported to play a role in transcriptional regulation, epigenetic remodeling, and other processes [
25].
To further investigate the role of model genes in severe asthma, we constructed an miRNA-mRNA regulatory network. The results showed that all genes, except KMT2B, were regulated by multiple miRNAs, suggesting complex regulatory relationships. In addition, predicted drugs also provide a basis for the future treatment of severe asthma.
We found that differentially expressed CRs are mainly involved in cell cycle pathways. Severe asthma is characterized by proliferation of airway smooth muscle (ASM) [
12]. Stimulation, including growth factors and extracellular proteins, regulates mitosis, which in turn induces ASM cell proliferation [
42]. The patients included in this study were partially treated with ICS or oral corticosteroids (OCS) in a previous study (Sánchez‐Ovando et al., 2021). The anti-asthmatic approach described above is an effective inhibitor of ASM cell proliferation. Corticosteroids inhibit the signaling pathways of cell cycle progression (Ammit and Panettieri Jr, 2001). Differentially expressed CRs have also been found to be involved in lysine degradation. Lysine residues can increase pro-inflammatory factor activity and affect collagen synthesis. Thus, lysine degradation can modulate airway inflammation and airway remodeling, which are key pathogenic features of asthma [
21]. Drugs that target lysine may be important in the treatment of severe asthma.
CRs control chromatin structure and function by catalyzing and binding histone modifications and are regulators of epigenetics [
30]. Asthma patients were found to have enhanced histone acetyltransferases activity and reduced histone deacetylases activity. These modifications may lead to increased expression of genes associated with the inflammatory response profile of asthma [
16]. Another study related to differentially expressed chromatin-modifying enzymes found that cigarette smoke differentially affected the expression of epigenetic regulators in patients with chronic obstructive pulmonary disease, further regulating the expression of target genes [
36]. This study is the first to investigate the role of differentially expressed CRs in severe asthma, which may provide new targets for the treatment of asthma in the future.
This study had some limitations. First, the sample size may not be sufficiently representative. Second, the results were not experimentally validated. Moreover, multiple prospective studies are still needed.
In conclusion, this study constructed a risk model with good predictive performance by screening for differentially expressed CRs between subjects with severe asthma and healthy individuals and by selecting hub CRs among them. The results of this study provide new insights into the mechanisms underlying CRs in severe asthma.
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