A Transcriptional Regulatory Loop of Master Regulator Transcription Factors, PPARG, and Fatty Acid Synthesis Promotes Esophageal Adenocarcinoma

We profiled esophageal adenocarcinoma 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, RNA-Seq, 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 or OE33 cells knock down PPARG 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 ChIP sequencing technology for studying master transcription factor (PPARG) in human esophageal adenocarcinoma cancer cell lines (Eso26 and OE33). Overall design: Esophageal Cancer cell lines were harvested, and ChIPseq was performed using transcription factor antibodies. Eso26 and OE33 cells knock down PPARG with siRNA and control were generated by deep sequencing, in triplicate, using Illumina GAIIx.