Promoter Hypermethylation Promotes the Binding of Transcription Factor NFATc1, Triggering Oncogenic Gene Activation in Pancreatic Cancer

SIMPLE SUMMARY: High promoter methylation is not necessarily associated with shutting down gene activity but does sometimes correlate with increased transcription instead. In a genome-wide analysis, we studied gene regulation in pancreatic cancer. We identified a substantial number of genes with both promoter hypermethylation and high transcription levels. Subsequently, we screened for transcription factors that exhibit specific binding to such hypermethylated sequences. NFATc1 was one of several transcription factors that bound specifically methylated DNA motifs and triggered transcription. A particularly affected gene was ALDH1H3, whose expression has strong oncogenic implications. Activation of ALDH1H3 was due to a direct regulative process involving NFATc1 binding to its hypermethylated promoter. The results provide insights into the activation of gene transcription that is promoted by DNA methylation. ABSTRACT: Studies have indicated that some genes involved in carcinogenesis are highly methylated in their promoter regions but nevertheless strongly transcribed. It has been proposed that transcription factors could bind specifically to methylated promoters and trigger transcription. We looked at this rather comprehensively for pancreatic ductal adenocarcinoma (PDAC) and studied some cases in more detail. Some 2% of regulated genes in PDAC exhibited higher transcription coupled to promoter hypermethylation in comparison to healthy tissue. Screening 661 transcription factors, several were found to bind specifically to methylated promoters, in particular molecules of the NFAT family. One of them—NFATc1—was substantially more strongly expressed in PDAC than control tissue and exhibited a strong oncogenic role. Functional studies combined with computational analyses allowed determining affected genes. A prominent one was gene ALDH1A3, which accelerates PDAC metastasis and correlates with a bad prognosis. Further studies confirmed the direct up-regulation of ALDH1A3 transcription by NFATc1 promoter binding in a methylation-dependent process, providing insights into the oncogenic role of transcription activation in PDAC that is promoted by DNA methylation.