Systemic molecules in the process of asthma attack and recovery
To identify which factors were involved in the process of asthmatic patients, we analyzed the transcriptome data of GSE19301 data. Compared with the quiet group, Toll like receptor and NOD like receptor signaling pathway in the exacerbation group were activated (Fig. 1A). Compared with the follow-up group, NOD like receptor signaling pathway and apoptosis in the exacerbation group were activated (Fig. 1B). The results showed that there were the same regulatory mechanism and different molecular changes in the process of asthma from quiet to exacerbation to follow-up. Therefore, we compared the gene expression of three groups. There were 2194 differentially expressed genes (DEGs) between exacerbation and quiet groups (Fig. 1C). There were 1376 DEGs between exacerbation and follow-up groups (Fig. 1D). These results indicated that some genes and signaling pathways played crucial roles in the process of asthma from tranquility to exacerbation and then to tranquility.
Identifying asthma-associated PPI modules from DEGs
To further explore the interactions of differentially expressed genes in the process of exacerbation to recovery, we mapped the common genes in the two groups of DEGs into PPI network. 838 common genes were mapped into PPI network. Next, the module searching procedure identified 7 modules (Figure S1). The distribution of the genes with the highest or lowest expression level of exacerbation group in the module compared with quiet or follow-up was shown by heatmap (Fig. 2A). Up regulated genes of exacerbation and quiet were all in M2, and the down regulated genes were all in M5, respectively (Fig. 2B). Similarly, the up regulated genes of exacerbation and follow-up were all in M2, and the down regulated genes were all in M5 (Fig. 2C). Therefore, M2 genes may promote asthma, while M5 genes may inhibit asthma.
On the other hand, hub gene of each module by the degree in the module was screened (Table 2). Depending on the expression of hub genes in three groups of asthma, ENO1, OAS3 and TLR4 were the highest expressed in exacerbation, while HSP90AB1, HSPA9, PTCD3 and UBA52 were the lowest expressed in exacerbation (Fig. 2D). Therefore, they are considered to be potential genes for positive or reverse regulation of asthma exacerbation. Importantly, we verified the expression of these key genes during the exacerbation of asthma by qPCR (Fig. 2E). In addition, the results of correlation analysis also proved that there was a significant negative correlation between high or low expression genes in exacerbation (Fig. 2F). These results suggested that key genes can regulate the exacerbation of asthma, which may be used as a biomarker of asthma exacerbation for further study.
Table 2: The hub genes of modules for the disorder gene in the process of asthma deterioration to recovery
Module
|
Symbol
|
m1
|
UBA52
|
m2
|
OAS3
|
m3
|
TLR4
|
m4
|
HSP90AB1
|
m5
|
PTCD3
|
m6
|
ENO1
|
m7
|
HSPA9
|
Biological function and signal pathway involved in the process of asthma
To identify the biological functions and signaling pathways involved in the progression of asthma, module genes were enriched and analyzed. A total of 1741 BP, 113 CC, 232 MF and 65 KEGG signaling pathways were enriched by the module genes. Among them, genes mainly enriched in activation of the innate immune response and other immune inflammatory functions (Fig. 3A, B, C). Also enriched in Toll like receptor signaling pathway, regulation of cellular amine metallic process signal pathways (Fig. 3D). In the up-regulated or down-regulated pathway, we found that NOD − like receptor signaling pathway was activated in exacerbation group, but decreased in quiet and follow-up (Fig. 3E, F). ENO1, OAS3 and TLR4 were mainly enriched in coenzyme metallic process, nucleotidyltransferase activity, regulation of inflammatory response and others. HSP90AB1, HSPA9, PTCD3 and UBA52 were mainly involved in response to interleukin-4, response to interleukin-12, positive regulation of NF-kappaB transcription factor activity and others. In addition, the functional similarity among PTCD3, OAS3 and ENO1 is high (Fig. 3G).
Transcription factors (TF) regulating dysfunctional molecules
Transcription regulation played an important role in the progress of diseases. Since we had observed that the module genes were associated with the exacerbation and recovery of asthma. We obtained 76 transcription factor regulatory module genes (Fig. 4A). The results of correlation analysis identified the transcription factors STAT1 was highly correlated with the module genes, including XAF1, PSMB9, IFIT3 and IRF7 (Fig. 4B). Therefore, we believed that STAT1 was an important regulatory role in the pathogenesis of asthma.