Reducing N6AMT1-mediated 6mA DNA modification promotes breast tumor progression via transcriptional repressing cell cycle inhibitors

Jiongyu Chen,Yiteng Huang,Jinfeng Ning,Wei Liu,Yixuan Zhuang,Ping Wang,Donghong Zhang,Xueqiong Lin,Lin Peng

doi:10.1038/s41419-022-04661-8

Abstract

DNA N6-methyladenosine (6mA) is a novel epigenetic signaling modification in humans and has been implicated in the progression and tumorigenesis of several cancers. However, the function and mechanism of 6mA in breast cancer (BC), the most common cancer among women, are unclear. Here, we found that decreases in N6AMT1 correlated with the extent of 6mA in clinical BC tissues and predicted a worse survival of BC patients. Functionally, knockdown of N6AMT1 markedly reduced 6mA in DNA and promoted colony formation and migration of BC cells, whereas overexpression of N6AMT1 had the opposite effect. Moreover, silencing of N6AMT1 reduced 6mA modification and enhanced the growth of BC cells in vitro and tumors in vivo. 6mA immunoprecipitation sequencing (6mA-IP-seq), RNA-seq, 6mA-IP-PCR, and bioinformatics analysis indicated that N6AMT1 was a functional methyltransferase for genomic 6mA DNA modifications and related to gene transcriptional activity. Critical negative regulators of the cell cycle, such as RB1, P21, REST, and TP53 were identified as targets of N6AMT1 in BC. These results suggest N6AMT1 enhances DNA 6mA levels to repress tumor progression via transcriptional regulation of cell cycle inhibitors.

Highlights

Breast cancer (BC) is the most frequent cancer type among women and remains the leading cause of cancer-related death worldwide [1]
ALKBH1 expression was not prognostic (Fig. S1C). These results suggest a reduction of N6AMT1 correlates with DNA 6mA, tumor progression, and poor prognosis of BC patients
Reduction of N6AMT1 correlates with reduced DNA 6mA, enhanced tumor progression, and poor prognosis of BC patients To assess the clinical significance of DNA 6mA in BC development, we performed an ELISA assay for 6mA on our two BC cohorts

Summary

BACKGROUND

Breast cancer (BC) is the most frequent cancer type among women and remains the leading cause of cancer-related death worldwide [1]. Aberrant epigenetic landscapes, such as DNA methylated on cytosine residues at the 5 positions (5mC), histone modification, non-coding RNA, and microRNAs have been repeatedly implicated in BC tumor initiation and progression [4–6]. Several clinical studies have investigated the efficacy of DNA methyltransferase and histone deacetylase inhibitor administration as monotherapy for BC [5, 9]. These epi-drugs have shown limited antitumor efficacy at the maximum tolerated doses, suggesting the unsuitability of this approach. Functional role, and underlying mechanism of 6mA DNA modification in the development and progression of BC, we first analyzed 6mA and its regulator levels in clinical BC cohorts.

MATERIALS AND METHODS

RESULTS

Chen et al 4

DISCUSSION

ETHICS STATEMENT