Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

We profiled fresh-frozen esophageal tumor and normal samples and cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematically modeling was performed to establish (super)-enhancers landscapes and inter-connected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs was investigated by ChIP-Seq, RNASeq, 4C-Seq and luciferase assay. Biological functions of candidate factors were evaluated by measuring cell proliferation, colony formation, cell apoptosis and xenograft growth. Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. Here, we aim to compare of Eso26 cells knock down HNF4A with siRNA and control transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. We also report the application of circular chromatin conformation capture (4C) sequencing technology for studying master transcription factor (HNF4A) in human esophageal adenocarcinoma cancer cell lines (Eso26). Esophageal Cancer and normal cell lines and fresh-frozen tissues were harvested, and ChIPseq was performed using H3K27Ac and transcription factor antibodies. Eso26 cells knock down HNF4A with siRNA and control were generated by deep sequencing, in triplicate, using Illumina GAIIx. 4C sequencing analysis in espohageal adenocarcinoma cell line.