Introduction: Emerging evidence that epigenetics converts alterations in nutrient and metabolism into heritable pattern of gene expression has profound implications in understanding human physiology and diseases. Non-alcoholic fatty liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome including obesity and diabetes which elevate the risk of hepatocellular carcinoma (HCC). The metabolites derived from excessive insulin, glucose and lipid may perturb epigenetic gene regulation through DNA methylation, histone modifications, and RNA interference, leading to activation of pro-inflammatory signaling and oncogenic pathways. Transcriptional and chromatin patterns are mostly interrogated by chromatin immunoprecipitation (ChIP). However, conventional ChIP protocols necessitate the use of large numbers of cells and usually limit to the studies in cell lines, which may display epigenetic patterns distinct from primary tumors.
Aims and methods: To study chromatin deregulation in primary human NAFLD-related HCC tumor and adjacent non-tumor tissues, we performed nanoscale ChIP sequencing (nano ChIP-seq), which allows genome-wide location of histone modifications for scanty materials, of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) for active promoters and enhancers, respectively. We also integrated the nano ChIP-seq profiles with transcriptomic data from TCGA and in-house cohorts.
Results and summary: We found that primary human HCC tumors were associated with increased H3K4me3 occupancy, which occurred predominantly nearby the transcription start sites. H3K4me3-occupied promoters were enriched with signal transducer and activator of transcription (STAT) binding sites, which is in accordance with the crucial role of interleukin 6/STAT3 signaling in NAFLD-HCC initiation and progression. Moreover, tumor-specific H3K4me3 and H3K27ac profiles correlated with gene over-expression, including novel STAT3-driven oncogenes e.g. UBE2C and PLK1 in HCC. In summary, our findings demonstrated the feasibility of profiling chromatin using limited HCC tissues and identified aberrant promoter and enhancer regulatory elements associated with NAFLD-related hepatocarcinogenesis.
Acknowledgements: This project was supported by the University Grants Committee through the Collaborative Research Fund C4017-14G, Theme Based Research Scheme T12-403/11-1 and General Research Fund 14102914.
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Citation Format: Feng Wu, Yingying Lee, Sau Dan Lee, Patrick Tan, Nathalie Wong, Kevin Yuk-Lap Yip, Kai F To, Alfred Sze Lok Cheng. Nanoscale ChIP-seq analysis in primary hepatocellular carcinoma tissues reveals tumor-specific chromatin deregulation for oncogene activation. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4519.