Differential gene expression profiling by deletion of GFI1 super-enhancer (GFI1-SE-KO) upon treatment of a LSD1 inhibitor NCD38 in HEL cells

Activation of GFI1-super-enhancer (GFI1-SE) by a LSD1 inhibitor NCD38 was relevant to myeloid differentiation and antileukemia effect in human erythroleukemia cells (HEL cells). Thus, we investigated the role of GFI1-SE upon NCD38 treatment in HEL cells. We established three independent sublines with bi-allelic deletion of GFI1-SE (CCE2 #114, #141, and #216) using CRISPR-Cas9 genome editing system in HEL cells and a classical limiting dilution method. Control sublines (Ctrl C1, C2, and C5) were established by transfection of parent vector and limiting dilution. After treatment of each subline with DMSO or NCD38 (LSD1i) for 24 hours, these gene expression profiling data were obtained. Two target-specific oligonucleotides were designed to cleave upstream and downstream sites of the GFI1-SE, and were inserted into the entry site of the CRISPR-CAS9 genome editing vector (pX330-U6-Chimeric_BB-CBh-hSpCas9, Addgene, plasmid ID: 42230). Oligonucleotides for site-specific chromatin cleavage of target regions were designed using a bioinformatics tool (https://chopchop.rc.fas.harvard.edu/). Both vectors were transfected into HEL cells using the Amaxa nucleofection technology. After limiting dilution and genotype screening, three independent sublines with bi-allelic deletion of the GFI1-SE (delGFI1-SE) were established. For control sublines, the parent (non-inserted) CRISPR-CAS9 genome editing vector was used. After treatment of each subline with DMSO or NCD38 (LSD1i) for 24 hours, these gene expression profiling data were obtained.