DNA hypermethylation contributes to colorectal cancer metastasis by regulating the binding of CEBPB and TFCP2 to the CPEB1 promoter

Keke Shao,Ingrid Glurich,Zhao Zhang,Yanyun Ma,Shicheng Guo,Qing Jin,Jianfeng Zhang,Shaoqing Ju,Fei Qian,Weifeng Ding,Weilin Pu

doi:10.1186/s13148-021-01071-z

Abstract

BackgroundAberrant DNA methylation has been firmly established as a factor contributing to the pathogenesis of colorectal cancer (CRC) via its capacity to silence tumour suppressor genes. However, the methylation status of multiple tumour suppressor genes and their roles in promoting CRC metastasis are not well characterised.MethodsWe explored the methylation and expression profiles of CPEB1 (the gene encoding cytoplasmic polyadenylation element-binding protein 1), a candidate CRC tumour suppressor gene, using The Cancer Genome Atlas (TCGA) database and validated these results in both CRC cell lines and cells from Han Chinese CRC patients (n = 104). The functional role of CPEB1 in CRC was examined in experiments performed in vitro and in vivo. A candidate transcription factor capable of regulating CPEB1 expression was predicted in silico and validated by luciferase reporter, DNA pull-down, and electrophoretic mobility shift assays.ResultsHypermethylation and decreased expression of CPEB1 in CRC tumour tissues were revealed by TCGA database. We also identified a significant inverse correlation (Pearson’s R = − 0.43, P < 0.001) between promoter methylation and CPEB1 expression. We validated these results in CRC samples and two CRC cell lines. We also demonstrated that up-regulation of CPEB1 resulted in significantly decreased tumour growth, migration, invasion, and tumorigenicity and promoted tumour cell apoptosis both in vitro and in vivo. We identified the transcription factors CCAAT enhancer-binding protein beta (CEBPB) and transcription factor CP2 (TFCP2) as critical regulators of CPEB1 expression. Hypermethylation of the CPEB1 promoter resulted in a simultaneous increase in the capacity for TFCP2 binding and a decreased likelihood of CEBPB binding, both of which led to diminished expression of CPEB1.ConclusionsOur results identified a novel tumour-suppressive role of CPEB1 in CRC and found that hypermethylation of the CPEB1 promoter may lead to diminished expression due to decreased chromatin accessibility and transcription factor binding. Collectively, these results suggest a potential role for CPEB1 in the diagnosis and treatment of CRC.

Highlights

Colorectal cancer (CRC) is the third most common cancer diagnosed and the second leading cause of cancer-related deaths in the USA [1, 2]
We found that all nine of the CpG sites located within 1,500 base pairs of the transcription start site (TSS1500, including the promoter region) were significantly hypermethylated in colorectal cancer (CRC) tumours compared to the para-tumour tissue (Fig. 1a, b)
To confirm the robustness of the targeted bisulfite sequencing method, we examined the methylation status of SEPTIN9, a gene that has been widely reported to be hypermethylated in CRC (Fig. 1f)

Summary

Introduction

Colorectal cancer (CRC) is the third most common cancer diagnosed and the second leading cause of cancer-related deaths in the USA [1, 2]. Invasive metastatic disease in the liver or other organs occurs in 30–60% of patients diagnosed with CRC. There are very few effective therapeutic strategies that can be used to treat CRC patients with distant metastases. This is primarily due to a lack of molecular drug targets and/or any clear understanding of molecular mechanisms underlying the emergence of its invasive potential and the establishment of metastatic disease. Aberrant DNA methylation has been firmly established as a factor contributing to the pathogenesis of colorectal cancer (CRC) via its capacity to silence tumour suppressor genes. The methylation status of multiple tumour suppressor genes and their roles in promoting CRC metastasis are not well characterised

Methods

Results

Conclusion