Aberrant methylation of ATG2B, ATG4D, ATG9A and ATG9B CpG island promoter is associated with decreased mRNA expression in sporadic breast carcinoma

• The methylation status of ATG2B, ATG4D, ATG9A and ATG9B and the relationship of their expression levels in breast carcinoma
• Progress on the relationship between ATG2B, ATG4D, ATG9A and ATG9B regulation to tumorigenesis
• Potential new way of thinking towards autophagy regulatory networks
• Offer a new therapeutic target towards cancer biotherapy

Epigenetic modifications are critical determinants in tumor initiation and progression. This study aims to detect the promoter methylation status and the mRNA expression levels of ATG2B, ATG4D, ATG9A and ATG9B, and then to explore their relationship in invasive ductal carcinomas (IDCs) and matched normal tissues (MNTs) of the breast. Methylation was observed as follows: 61.0% in ATG2B, 46.8% in ATG4D, 56.4% in ATG9A, and 74.0% in ATG9B of IDCs. Meanwhile, their mRNA expression levels of the IDCs was lower than that of the MNTs (P < 0.001, P = 0.019, P < 0.001 and P < 0.001, respectively). Methylated IDCs of ATG2B, ATG9A, ATG9B and unmethylated ATG4D, ATG9B showed significantly lower expression values compared to the MNTs (P = 0.003, P < 0.001, P < 0.001, P = 0.014 and P = 0.002, respectively). The methylations of ATG2B and ATG9B were related to their lower expression levels in IDCs (P = 0.017 and P = 0.023). Moreover, ATG2B methylation was positively associated with the grade (P = 0.024) and TNM stage (P = 0.015); Methylation of ATG4D and ATG9A was positively correlated to lymph node involvement (P = 0.012 and P = 0.018), while methylation of ATG9B appeared susceptible to CK5/6 positive status and deteriorated TNM stages (P = 0.003 and P = 0.012). Moreover, the decreased expression of ATG2B was related to the ER and PR status (P = 0.004 and P = 0.003). The ER, HER-2 and lymph node metastasis status are the determinants to reducing the expression of ATG4D, ATG9A and ATG9B (P = 0.026, P = 0.010 and P = 0.011, respectively). This study highlights the transcriptional inactivation mechanisms of ATG2B, ATG4D, ATG9A and ATG9B promoter methylation status and the possible origin of autophagy signal pathway repression in IDCs.