GSE106378
HNF4alpha P1 and P2 isoforms regulate different gene networks in the colorectal cancer cell line Caco2/15.
The nuclear receptor HNF4alpha is a master regulator of gene transcription in intestinal epithelial cells where P1 and P2 isoforms are expressed. HNF4alpha has been associated with colorectal cancer  where its role remains controverisal since both tumor suppressor and  oncogene characteristics have been observed. Evidences gathered from mouse models suggested however that this controversy on HNF4alpha function in colorectal cancer could be explained by the different functions of its two isoforms classes. In order to clarify this hypothesis in a human context, we downregulated the expression of HNF4alpha P1 or P2 isoforms using isoforms specific shRNA in the colorectal cancer cell line Caco2/15. Transcriptomic data were obtained by RNA-seq from these shRNA cell populations and compared to a non-target shRNA control. Overall design: Colorectal cancer cell line Caco2/15 (clone of Caco-2) was infected for 48 hours with lentiviral shRNAs targeting HNF4alpha P1 or P2 isoforms classes or a control shRNA targeting no human genes. Lentiviruses were removed and cells incubated for another 24 hours before extracting RNA. Cells reached one day post-confluence at the time RNA was extracted. RNA librairies were prepared using TrueSeq mRNA kit (Illumina) and paired reads generated using Illumina Hiseq 2000/2500 sequencer. Base calls were made using Illumina CASAVA pipeline. Three biological independant replicates were analyzed in each condition.