Promoter Hypermethylation of ARID1A Gene Is Responsible for Its Low mRNA Expression in Many Invasive Breast Cancers

Abstract

ARID1A (AT-rich interactive domain 1A) has recently been identified as a tumor suppressor gene. Its mRNA expression is significantly low in many breast cancers; this is often associated with more aggressive phenotypes. However, the underlying molecular mechanism for its low expression has not been fully understood. This study was undertaken to evaluate the contribution of gene copy number variation, mutations, promoter methylation and histone modification to ARID1A’s low expression. 38 pairs of breast invasive ductal carcinomas and their normal breast tissue counterparts from the same patients were randomly selected for gene expression and copy number variation detection. Promoter methylation and histone modification levels were evaluated by MeDIP-qPCR and ChIP-qPCR, respectively. PCR product Sanger sequencing was carried out to detect the exon mutation rate. Twenty-two out of 38 invasive ductal carcinomas in the study (57.9%) revealed ARID1A mRNA low expression by realtime RT-PCR. The relative promoter methylation level was, significantly higher in ARID1A mRNA low expression group compared with its high expression group (p<0.001). In the low expression group, nineteen out of 22 invasive ductal carcinomas (86.4%) exhibited ARID1A promoter hypermthylation. In addition, the promoter hypermethylation was accompanied with repressive histone modification (H3K27Me3). Although five out of 38 invasive ductal carcinomas (13.2%) exhibited loss of ARID1A gene copy number by realtime PCR and nine exon novel mutations are seen from eight out of 33 invasive ductal carcinomas (24.2%), there was no statistically significant difference in both ARID1A mRNA low and high expression groups (p = 0.25,and p = 0.68, respectively). We demonstrate that promoter hypermethylation was the main culprit for ARID1A mRNA low expression in invasive ductal carcinomas. The influence of mutation and copy number variation on the expression were statistically insignificant at mRNA level, and were, therefore, not considered the main causes for ARID1A mRNA low expression in invasive breast cancer.

Loss of ARID1A Activates ANXA1, which Serves as a Predictive Biomarker for Trastuzumab Resistance

“…Although ARID1A mutation frequency in breast cancer appears to be modest (some 4%; ref. 6), ARID1A loss may be caused via other mechanisms, such as promoter hypermethylation and DNA copy number loss (41)(42)(43). However, our data do not rule out the possibility that induction of ANXA1 levels is also caused by oncogenic signaling pathways that are independent of ARID1A loss.…”

Downregulation of ARID1A, a component of the SWI/SNF chromatin remodeling complex, in breast cancer

“…Recently, Zhang et al . reported that promoter hypermethylation of the ARID1A gene is responsible for its low mRNA expression in many invasive breast cancers 25. These findings encouraged us to score the ARID1A immunoreactivity of invasive breast cancer to evaluate the prognosis value of ARID1A in invasive breast cancers.…”

Loss of ARID1A expression and its relationship with PI3K-Akt pathway alterations, TP53 and microsatellite instability in endometrial cancer

“…This explanation may be viable, as CpG islands have been identified on the ARID1A promoter and ARID1A promoter hypermethylation has been reported recently in invasive breast cancer. 38 However, several other studies have shown that ARID1A loss of expression is strongly associated with mutations in the ARID1A gene, and for endometrial cancer, the mutation rate corresponds with the frequency of ARID1A loss. 4,6,12,26 Moreover, promoter hypermethylation as inactivating mechanism of the ARID1A gene has not been reported in endometrial cancer.…”