Differential DNA methylation patterns of the PDE9A, SEPT8, ZNF323, CYSLTR1, TIGIT, ADORA2B, and CCDC88C genes at cross sectional levels in the validation cohort. (A) DNA methylation levels of the PDE9A gene body (+ 30,088 CpG site) were increased in ACO patients versus either pure COPD patients or healthy subjects (HS), and (B) negatively correlated with post-BD FEV1%predicted. (C) DNA methylation levels of the SEPT8 gene promoter region (− 47 CpG site) were decreased in ACO patients versus either pure COPD patients or HS, and (D) positively correlated with post-BD FEV1%predicted. (E) DNA methylation levels of the ZNF323 gene promoter region (− 296 CpG site) were increased in ACO patients versus either pure COPD patients or HS, and (F) also increased in all the COPD patients with frequent exacerbation versus those without frequent exacerbation or HS. (G) DNA methylation levels of the CYSLTR1 gene promoter region (+ 348 CpG site) were decreased in GOLD III-IV COPD patients versus GOLD I-II COPD patients. (H) DNA methylation levels of the CCDC88C gene body (+ 125,722 CpG site) were decreased in GOLD III-IV COPD patients versus GOLD I-II COPD patients. (I) DNA methylation levels of the ADORA2B gene body (+ 1339 CpG site) were decreased in GOLD III-IV COPD patients versus GOLD I-II COPD patients. (J) DNA methylation levels of the TIGIT gene promoter region (− 172 CpG site) were increased in GOLD III-IV COPD patients versus GOLD I-II COPD patients. **Compared between ACO and pure COPD patients, and adjusted by multivariate linear regression. ##Compared between ACO and healthy non-smokers (HS), and adjusted by multivariate linear regression. §Compared between COPD patients with GOLD I-II and GOLD III-IV, and adjusted by multivariate linear regression.