Background Chronic rhinosinusitis (CRS) and nasal polyps (NP) are closely related inflammatory airway diseases, and their co-occurrence is often associated with more persistent symptoms, frequent recurrence, and substantial respiratory morbidity. However, the extent to which CRS without and with NP (CRSsNP and CRSwNP) share genetic susceptibility—and which genetic mechanisms are disease-specific—remains poorly characterized.

Methods We conducted cross-population genome-wide association meta-analyses of overall CRS (including both CRSwNP and CRSsNP) and NP (a proxy for CRSwNP) using data from six biobanks. We estimated genome-wide genetic correlations between overall CRS, CRSwNP, and a spectrum of respiratory diseases. We applied five complementary gene-prioritization strategies to nominate CRS- and CRSwNP-associated genes and performed pathway enrichment analyses to infer implicated biological processes. For CRSwNP, we integrated single-cell transcriptomic data to characterize cell-type–specific expression of prioritized genes and used stratified LD score regression to quantify heritability enrichment across immune and epithelial annotations. To delineate shared versus disease-specific genetic signals, we performed three comparative analyses—local genetic correlation, CRSwNP-CRS colocalization, and genomic structural equation modeling. Finally, we performed proteome-wide Mendelian randomization to identify circulating proteins with putative causal effects on CRS and CRSwNP.

Results This GWAS meta-analysis identified 96 genome-wide significant loci for CRSwNP and 41 for overall CRS, prioritizing 92 and 39 candidate genes, respectively. CRSwNP and overall CRS showed shared genetic susceptibility (rg = 0.59; P = 6.8 × 10⁻¹□), while CRS exhibited broader genetic correlations across multiple respiratory disorders. Pathway analyses consistently implicated immune signaling albeit with disease-specific emphases and lipid-metabolism networks. Single-cell analyses demonstrated distinct expression of CRSwNP-prioritized genes across nasal epithelial and immune cell clusters, and immune annotations explained more CRSwNP heritability (enrichment score = 4.1; P = 0.010) than epithelial annotations (2.5; P = 0.072). Comparative genetic analyses highlighted multiple shared loci—including BACH2, CD247, FADS2, FOXP1, FUT2, GPX4, IL7R, NDFIP1, RAB5B, RORA, SMAD3, TSLP —as well as 3 CRSwNP-specific and 6 CRS-specific loci. Proteome-wide MR identified 10 and 8 putatively causal circulating proteins for CRSwNP and overall CRS, respectively, with protein TNFSF11, IL2RB, and STX4 associated with both conditions.

Conclusions This multi-population GWAS meta-analysis expanded genetic discovery for CRS and CRSwNP and showed substantial shared liability with distinct disease-specific components. Immune components explained a larger proportion of CRSwNP heritability than epithelial annotations, reinforcing the primacy of immune-driven mechanisms in polyp disease.

S.M.D. receives personal consulting fees from Tourmaline Bio, research support from RenalytixAI, and in-kind research support from Novo Nordisk and Amgen, all outside the scope of the current project. Other authors declare no conflicts of interests.

This study did not receive any funding.

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This study only used publically available data sources. All data used in the study have been cited.

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↵* Shuai Yuan and John C McVey share the joint first authorship.

↵# Michael G. Levin and Scott M. Damrauer shared the joint senior authorship.

The GWAS data generated in this study will be deposited in the NHGRI-EBI GWAS catalog database once the paper is published online.