# Identification and dual-center histological validation of EMT core genes in chronic rhinosinusitis with nasal polyps: an integrated multi-cohort transcriptomic and single-cell analysis

## TL;DR

This study identifies three key genes linked to tissue changes in nasal polyps, validated across multiple patient groups and confirmed through detailed tissue analysis.

## Contribution

The study introduces three robust EMT core genes validated across multiple cohorts and histologically confirmed in chronic rhinosinusitis with nasal polyps.

## Key findings

- SPP1, PTHLH, and IGFBP3 are consistently upregulated EMT core genes in CRSwNP across multiple datasets and dual-center validation.
- The three-gene model shows high accuracy (AUC 0.888–0.991) in predicting CRSwNP and is associated with immune infiltration and key pathways like TGF-β and inflammation.
- Histological validation confirms EMT-related changes linked to these genes, particularly in the eosinophilic endotype of CRSwNP.

## Abstract

Chronic rhinosinusitis with nasal polyps (CRSwNP) is highly heterogeneous. Epithelial–mesenchymal transition (EMT) is implicated in mucosal remodeling and postoperative recurrence, yet robust EMT biomarkers consistently validated across cohorts and by histology are lacking.

RNA-seq data from a Chongqing (CQ) cohort were integrated with multiple GEO datasets. After batch-effect correction, differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed. EMT-related candidates were obtained by intersecting results with the MSigDB EMT gene set. Core genes were identified using multi-algorithm feature selection (LASSO, SVM-RFE, and random forest). A three-gene model was constructed and externally validated. Single-cell transcriptomic data were used to define cellular sources of core genes, and immune infiltration and pathway activity were assessed. Regulatory networks (TF/miRNA) and compound–disease associations were predicted. Finally, expression was validated in dual-center clinical cohorts (CQ and Liaoning [LN]) by qRT-PCR and immunohistochemistry/immunofluorescence, and associations with SNOT-22 and the eosinophilic endotype were evaluated.

Twenty-five EMT-related candidate genes were identified. Multi-algorithm intersection highlighted SPP1, PTHLH, and IGFBP3 as EMT core genes, consistently upregulated in the training set, the external validation dataset, and dual-center specimens. The three-gene model achieved AUCs of 0.944–0.991 in the training set and 0.888–0.938 in the external validation dataset. Single-cell mapping indicated that SPP1 was primarily derived from myeloid cells, PTHLH from epithelial cells, and IGFBP3 enriched in fibroblasts. Higher core-gene expression was associated with increased immune infiltration and activation of TGF-β, hypoxia/glycolysis, and inflammation-related pathways. Histology supported EMT-associated phenotypic changes in CRSwNP, with stronger signals in the eosinophilic endotype. In CQ and LN cohorts, core-gene expression correlated with SNOT-22 (Spearman r = 0.402–0.569, P ≤ 0.021).

SPP1, PTHLH, and IGFBP3 are robustly validated EMT core genes in CRSwNP across multiple cohorts and dual-center histology, closely linked to immune microenvironment alterations and mucosal remodeling. These genes represent robust EMT-associated candidate biomarkers for future stratification efforts and mechanistic investigations.