Immune Gene Profiling Offers New Targets for CRSwNP Diagnosis & Treatment

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Approximately 10% of adults across the world experience chronic rhinosinusitis (CRS), making it one of the most common chronic inflammatory diseases, researchers noted in Scientific Reports. There are two main types of CRS: chronic rhinosinusitis with nasal polyps (CRSwNP) and without nasal polyps.

CRSwNP is often associated with asthma and allergic rhinitis. The inflammatory response, which is triggered by a wide variety of cells and cytokines, exacerbates the progression of this condition. Previous studies have demonstrated that eosinophils, neutrophils, macrophages, and other immune-related cells and genes play a role in the pathogenesis of CRSwNP; however, further research is necessary to gain a deeper understanding of this condition. Researchers aimed to accomplish this with the help of machine learning.

Data Collection

Datasets from the GEO database were used in this study, with the following search terms in all fields: chronic and rhinosinusitis or nasal polyps.

This strategy rendered two relevant datasets that they used throughout the study: GSE136825 and GSE36830.

GSE136825 included 28 inferior turbinate tissues obtained from healthy controls and 42 nasal polyp tissues collected from patients with CRSwNP. GSE36830 included six nasal polyp samples and six samples from healthy control subjects. They used data from GSE136825 as the training set and data from GSE36830 as the validation set.

The researchers also collected data about immune-related genes (IRGs) from the ImmPort database, resulting in 1,509 total IRGs.

Study Methods

 The study team analyzed differentially expressed genes (DEGs) between CRSwNP and inferior turbinate tissues. They filtered this data using a P value of less than 0.05, resulting in 660 DEGs intersecting with 1,509 IRGs. These were used to identify the differentially expressed immune-related genes (DIRGs).

Researchers analyzed these genes for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. After visualizing the results, they obtained human protein-protein interactions (PPIs) from the STRING database to construct a PPI network and built a DIRG prediction model.

Once these data collection and analysis tools were set up, the researchers recruited 32 study participants: 20 with CRSwNP and 12 healthy controls who needed septoplasty for a deviated septum. Using functional endoscopic sinus surgery or inferior turbinoplasty, they collected nasal polyps from CRSwNP patients and inferior turbinates from the controls.

No study participants received corticosteroids for 4 weeks prior to enrollment. Exclusion criteria included severe systemic disease, immunodeficiency, fungal sinusitis, and pregnancy.

Impact of Five Overlapping Genes

 Researchers cultured cells from each participant, extracting total RNA and isolating total protein. The tissue was then prepared for antigen retrieval and ELISA testing and analysis. They intersected 660 DEGs with 1,509 IRGs in the ImmPort database, obtaining 81 DIRGs, and analyzed the protein interactions of these DIRGs “using the STRING database to obtain PPI networks with interaction scores greater than 0.4.”

Using this data, they analyzed the correlation between expression levels of the DIRGs, finding strong correlations between CXCR1, CXCR2, and CXCR6.

Further analysis identified five overlapping genes—CXCR1, CCL13, PPBP, CCR3, and MMP9—that were examined and validated.

“The results of the principal component analysis (PCA) showed that these five candidate genes could clearly distinguish CRSwNP from controls, suggesting that they may play a key role in the diagnosis of CRSwNP,” the researchers wrote.

Significance of Immune Characteristics

 The study team also identified correlations between several different DIRGs and CRSwNP. For example, expression of CXCR1, CCL13, CCR3, and MMP9 genes was higher in patients with CRSwNP versus controls, whereas expression of PPBP was lower. There were also significant variations in M2 macrophages and mast cells between the groups.

The findings show that screening for DIRGs can benefit patients and clinicians by helping identify the most appropriate therapeutic treatments, according to the researchers, and underscore the significance of the immune characteristics of CRSwNP pathogenesis.

“This discovery provides valuable insights into the underlying mechanisms of CRSwNP and presents potential targets for future therapeutic investigations,” the study team wrote.