Microarray expression profile analysis of aberrant long non-coding RNAs in esophageal squamous cell carcinoma

Abstract

Increasing evidence indicates that long non-coding RNA (lncRNA) plays an important role in tumorigenesis. However, the function and regulatory mechanism of lncRNAs are still unclear in esophageal squamous cell carcinoma (ESCC). To address this challenge, we screened lncRNAs expression profiles in 3 pairs of ESCC and matched non-cancerous tissues by microarray assay and identified the relationship between lncRNAs expression in ESCC tissue and clinicopathological characteristics and prognosis of patients with ESCC. We found 182 lncRNAs that were significantly differently expressed in ESCC tissues versus the matched non-cancerous tissues. Gene ontology and pathway analysis results suggested that the primary biological processes of these genes were involved in extracellular matrix, immune responses, cell differentiation and cell proliferation. Through cis and trans analyzing, we found 4 lncRNAs (ENST00000480669, NONHSAT104436, NONHSAT126998 and NONHSAT112918) may play important roles in tumorigenesis of ESCC. The four lncRNAs were checked in 73 patients with ESCC. The results showed that they mainly related to tumor metastasis. Kaplan-Meier survival analysis showed that high expression of NONHSAT104436, NONHSAT126998 and low expression of ENST00000480669 were related to poor 3-year overall survival (P=0.003, 0.032 and 0.040, respectively). Multivariate analysis showed that NONHSAT104436 was an independent prognostic factor (P=0.017). Thus we concluded that, lncRNAs showed differently expression patterns in ESCC versus matched non-cancerous tissues, and aberrantly expressed lncRNA may play important roles in ESCC development and progression. Interestingly, the overexpression of NONHSAT104436 was tightly correlated with distant metastasis and, poor survival rate, which might indicate that NONHSAT104436 might play a very important part in ESCC tumor progression.

LncRNA‑ECM is overexpressed in esophageal squamous cell carcinoma and promotes tumor metastasis

“…Among the 39 lncRNAs with significant differences (FC>10) reported previously (12), due to the significant between-group difference, non-significant in-group difference (Fig. 1A) and higher abundance compared with its origin (Fig.…”

“…Therefore, it is crucial to identify differentially expressed lncRNAs in ESCC and investigate their function and underlying mechanism in ESCC metastasis. LncRNA-ENST00000589379 has been found to be highly expressed in ESCC tissues with undefined function by gene chips (12). In the present study, this novel lncRNA is referred to as lncRNA-ECM.…”

“…LncRNA-ECM (lncRNA ENST00000589379) is a newly discovered lncRNA, which exhibited high expression in the ESCC gene chip (12). Sequence analysis demonstrated that lncRNA-ECM was composed of 3,218 bp, and there were a number of cis-regulatory elements, binding sites and hypersensitive sites of DNase I in the region of the chromosome, indicating that the transcription status of this region was relatively active.…”

“…Microarray analysis (12 Cell culture and transfection. The human ESCC cell lines TE-1, KYSE150, Eca109, KYSE30, EC9706 and the normal human esophageal mucosal epithelial HET-1A cell line were purchased from Shanghai Meixuan Biotechnology (Shanghai, China) and cultured in RPMI-1640 (Corning Inc., Corning, NY, USA) medium containing 10% fetal bovine serum (GE Healthcare Life Sciences, Logan, UT, USA) in 5% CO 2 at 37˚C.…”

BRAF-activated non-protein coding RNA (BANCR) advances the development of esophageal squamous cell carcinoma via cell cycle

“…Unfortunately, the average 5-year survival rate of ESCC remains lower than 10% [19,20]. Recently, a greater number of studies have focused on the underlying mechanisms for how the development and progression of ESCC cells occurred [21][22][23].…”