RNA sequencing in LSD1 knockout hepatocellular carcinoma cell lines

We conducted functional analysis of the histone demethylase LSD1 to explore the possibility that this enzyme acts as a therapeutic target in HCC. According to immunohistochemical analysis, 232 of 303 (77%) HCC cases showed positive staining of LSD1 protein, and its expression was correlated with several clinicopathological characteristics such as AFP levels and HCV infectious. The survival curves for HCC using the Kaplan-Meyer method and the log-rank test indicated that positive LSD1 protein expression was significantly associated with decreased rates of overall survival (OS) and disease-free survival (DFS). Importantly, the multivariate analysis indicates that LSD1 expression was an independent prognostic factor for both overall and disease-free survival in patients with HCC. Knockdown of LSD1 using induced CRISPR/Cas9 system showed significantly lower number of colony formation units (CFUs) and growth rate in both SNU-423 and SNU-475 HCC cell lines compared to corresponding untreated cells. Moreover, LSD1 knockout decreases cells in S phase of SNU-423 and SNU-475 cells with increase levels of H3K4me1/2 and H3K9me1/2. To further identify the signaling pathways regulated by LSD1 in HCC, we performed transcriptome analyses using inducible LSD1 knockout HCC cell lines (SNU-423 and SNU-475). Overall design: RNA-sequencing of two groups (No doxycycline-treated and doxycycline-treated cell lines) each with 4 biological replicates.