Single-end RNA-seq using Ion Torrent; FOXO1 Knockdown; 2 biological replicates per condition; Huh-7 cells
Forkhead Box O-1 (FOXO1) is one of the key regulatory transcription factors capable of regulating many critical cellular functions, such as promoting apoptosis and inhibiting cell cycle progression thereby acting as a tumor suppressor. In hepatocellular carcinoma (HCC), FOXO1 has been shown to be downregulated in liver tissues, and the lower expression has been correlated with poor prognosis. This highlights the necessity of understanding the regulatory functions of FOXO1 in more depth. Various studies have focused on the role of non-coding RNAs (ncRNAs), mainly microRNAs, as upstream regulators of FOXO1 in HCC and how their dysregulation affects carcinogenesis. However, the role of FOXO1 as an upstream regulator of ncRNAs, specifically long non-coding RNAs (lncRNAs), remains an unexplored area of research that needs to be addressed. In this study, we aimed to dissect this interplay and to identify potential FOXO1-regulated lncRNAs which could possibly play a role in the pathogenesis of HCC. This was achieved through the analysis of publicly available ChIP-Seq data provided by ENCODE database, along with performing RNA sequencing after the knockdown of FOXO1 in Huh-7 cells. ChIP-Seq data analyses revealed a list of 982 promising lncRNAs that are possibly regulated by FOXO1. Analysis of the RNA sequencing data revealed 131 lncRNAs that were differentially expressed after FOXO1 knockdown. The intersection between ChIP-Seq data and RNA sequencing data showed an overall of 12 lncRNAs that were differentially expressed upon FOXO1 knockdown and also have a FOXO1 binding site in their promoter region, namely ZFAS1, LINC00862, SNHG32, LINC01962, SNHG12, 1QCH-AS1, LINC00324, DCXR-DT, GLUD1P2, FAB5P3, JPX, and SMPD4BP. In conclusion, 12 lncRNAs were identified as potential downstream targets of FOXO1, suggesting that those lncRNAs could mediate FOXO1 functions in HCC.