Genotype–phenotype segregation in chronic rhinosinusitis with nasal polyp and associated comorbid severe asthma: multivariate clustering of interleukin-4, interleukin-6, interleukin-13, and TNF-α variants with type 2 biomarkers and clinical traits

Objectives This study examined the association between IL-4, IL-6, IL-13, and TNF-α gene polymorphisms and chronic rhinosinusitis with nasal polyps (CRSwNP) in patients with comorbid severe asthma and explored how these variants aligned with inflammatory phenotypes. Methods Eighty-one patients with CRSwNP and asthma were compared with 120 healthy controls using PCR-RFLP analysis of IL-4 (C590T), IL-6 (− 174G/C), IL-13 (R130Q), and TNF-α (G308A) polymorphisms. Clinical and biomarker data were available for 65 patients and were used for phenotype–genotype clustering. Results TNF-α polymorphisms demonstrated the strongest association with the combined CRSwNP-severe asthma phenotype. IL-6 polymorphisms also showed a significant association, with the GG genotype significantly enriched in CRSwNP-severe asthma patients (OR 2.39, p = 0.03), and both the dominant and recessive inheritance models demonstrated increased odds of disease. IL-4 showed no significant genotype differences, although the CT + TT recessive model demonstrated a borderline association (OR 1.73, p = 0.05). IL-13 genotypes did not differ significantly between groups, although the dominant and recessive models showed non-significant trends toward increased disease susceptibility. For TNF-α, the GG genotype was markedly enriched in patients and showed the strongest association with disease (OR 5.30, p < 0.001), with the dominant model demonstrating a similar association. Logistic regression identified age, IL-4 CT + TT, IL-6 CC + CG, IL-13 RQ + RR, and TNF-α AA + AG as independent predictors of CRSwNP-severe asthma. In adjusted analyses, IL-13 RQ + RR (OR 2.24, p = 0.03) and IL-4 CT + TT (OR 1.89, p = 0.05) remained associated with increased odds of CRSwNP-severe asthma, whereas IL-6 CC + CG (OR 0.36, p = 0.04) and TNF-α AA + AG (OR 0.10, p < 0.001) were associated with lower odds of the combined CRSwNP-severe asthma phenotype in the adjusted regression model. Clinically, patients demonstrated a predominantly Type 2-high (T2 high) inflammatory profile, with elevated IgE, blood eosinophils, and FeNO, and a high prevalence of severe asthma and allergic rhinitis. Multivariate clustering revealed three biologically distinct CRSwNP phenotypes: a dominant T2-high group enriched with IL-4, IL-6, IL-13, and TNF-α variants; an intermediate mixed-inflammation group; and a low-inflammation group with sparse cytokine polymorphisms. An ordination plot showed how these variants aligned along major genetic axes, illustrating coordinated and independent contributions of interleukin and TNF polymorphisms to patient divergence. Conclusion IL-4 (C590T), IL-6 (− 174G/C), IL-13 (R130Q), and TNF-α (G308A) polymorphisms demonstrated genotype-specific associations with the combined CRSwNP-severe asthma phenotype under different inheritance models. The TNF-α GG genotype exhibited the strongest genetic association, whereas IL-4 and IL-13 variants remained independently associated with increased disease susceptibility in the adjusted regression analyses. Genotype–phenotype clustering revealed structured biological heterogeneity, with specific cytokine variants aligning with the most pronounced T2-high inflammatory profiles. These findings provide additional insight into the immunogenetic heterogeneity of the combined CRSwNP-severe asthma phenotype and should be considered exploratory pending validation in larger independent cohorts.