Abstract 2629: N6AMT1-mediated DNA 6mA modification in DNA repetitive elements LINE-1 dynamically regulates the IFN signal pathway in colorectal cancer

Abstract Background: DNA N6-methyldeoxyadenosine (6mA) modification is the most prevalent DNA modification in prokaryotes, like bacteria, which participates in the host defense system. However, the presence and function of DNA 6mA in eukaryotes remains elusive. Many studies have reported that DNA 6mA modification is distributed across the genome and regulates transcription and the activity of transposable elements, in which the DNA 6mA methyltransferases and demethylases are involved, including the methyltransferase N6AMT1. LINE-1 is a genome-wide DNA repetitive element that acts as a diagnostic and prognostic biomarker for colorectal cancer. Therefore, we aimed to map the DNA 6mA in LINE-1 and investigate its role in the colorectal cancer (CRC) development. Methods: The restriction-enzyme-digestion assay followed by quantitative PCR (6mA-RE-qPCR) was used to evaluate the LINE-1 DNA 6mA levels in the tumor and normal tissues. The DNA Nanopore sequencing was utilized to determine DNA 6mA and 5mC modifications. After the knockdown of N6AMT1, the dynamic changes of LINE-1 DNA 6mA methylation and RNA transcription under various stresses were determined by 6mA-RE-qPCR and qPCR, and the subsequent RNA-seq was performed to explore the downstream regulated pathways. Results: The DNA 6mA methylation in LINE-1 is highly variant in the tumor and normal tissues, and it was significantly less prevalent in tumor tissues. The genomic distribution of LINE-1 DNA 6mA is significantly different from that of LINE-1 5mC. The LINE-1 DNA 6mA methylation and RNA transcription levels were dynamically changed in response to various stimuli, including 5-FU and H2O2. Knockdown of N6AMT1 downregulated LINE-1 DNA 6mA methylation and RNA transcription, promoted the proliferation, migration and invasion of CRC cells in vitro, and suppressed the IFN-gamma pathway. The co-culture assay showed N6AMT1 facilitated chemotaxis of macrophages and cytotoxicity of T cells via the IFN-gamma signal pathway. Conclusions: The heterogeneity of DNA 6mA methylation in LINE-1 and its dynamic change in response to stimuli indicate a biological role of LINE-1 6mA methylation in the primary and adaptive tumor heterogeneities, which provides a novel insight into cancer development. The N6AMT1-mediated DNA 6mA modification in LINE-1 regulates CRC development through the IFN-gamma pathway. Keywords: N6AMT1, LINE-1, DNA 6mA methylation, colorectal cancer Citation Format: Ze Yuan, Xiaoxia Liu, Xiaolin Wang, Yanxin Luo, Huichuan Yu. N6AMT1-mediated DNA 6mA modification in DNA repetitive elements LINE-1 dynamically regulates the IFN signal pathway in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2629.