A long non-coding RNA LINC00094 regulates the transcriptional expression of lipid metabolism-related genes as a new member of core regulatory circuitry in esophageal squamous cell carcinoma

LINC00094 as a new supper-enhancer (SE)-related long non-coding RNA is associated with poor overall survival of patients with esophageal squamous cell carcinoma (ESCC). However, the transcriptional regulatory mechanism of LINC00094 and the molecular mechanisms by which LINC00094 affects the phenotype of ESCC remains unclear. Here, we found that LINC00094 promoted the proliferation of ESCC cells both in vitro and in vivo. LINC00094 knockdown significantly reduced the expression profiles of transcription activators including transcription factor 3 (TCF3) and Kruppel like factor 5 (KLF5) and lipid metabolism-related genes. Mechanically, TCF3 and KLF5 formed a core regulatory circuitry (CRC) that bound to the SEs of LINC00094 and to their own SEs to regulate the transcriptional expression in a positive feedback loop. LINC00094 recruited TCF3 and KLF5 to form a ternary complex, which forms a new CRC with TCF3 and KLF5 that regulated its own transcription as well as lipid metabolism-related genes. Knockdown of any or all three genes inhibited the expression of genes related to lipid synthesis and consistently reduced total lipid droplet levels. Treatment with SEs inhibitors (THZ1 and JQ1) effectively inhibited the formation of this CRC and the production of lipid droplets in ESCC cells. The high-risk group of CRC-associated signatures were closely associated with poor prognosis in patients with ESCC. Our findings suggest that LINC00094 is involved in the CRC by forming a complex with TCF3 and KLF5, and this regulation model can affect the phenotype of ESCC cells by controlling the expression of lipid metabolism-related genes. 1. We identified a novel functional lncRNA-LINC00094 for esophageal squamous cell carcinoma. 2. LINC00094 forms a complex with the core transcription factors TCF3 and KLF5, thereby forming a core regulatory circuitry to participate in transcriptional regulation in ESCC. 3. A core regulatory circuitry mediated by LINC00094 regulates lipid metabolism in ESCC. ### Competing Interest Statement The authors have declared no competing interest. * ### Abbreviations AUC : area under the curve ChIP-seq : chromatin immunoprecipitation co-IP : co-immunoprecipitation CRC : core transcriptional regulation circuitry DEG : differentially expressed gene ESCC : esophageal squamous cell carcinoma GEO : Gene Expression Omnibus GO : gene ontology H3K27ac : Acetylation at the 27th lysine residue of the histone H3 protein KLF5 : kruppel like factor 5 IGV : integrative genomics viewer LASSO : least shrinkage and selection operator lncRNA : long non-coding RNA NC : Negative control OS : overall survival RIP : RNA binding protein immunoprecipitation ROC : receiver operating characteristic curve RT-qPCR : reverse transcriptase-quantitative real-time PCR SE : super-enhancer SEM : standard error of the mean TCF3 : transcription factor 3 TF : transcription factor