Tumor Biology

, Volume 37, Issue 10, pp 13091–13100 | Cite as

Transcriptome profiling of lncRNA and co-expression networks in esophageal squamous cell carcinoma by RNA sequencing

  • Yuan Li
  • Xuejiao Shi
  • Wenhui Yang
  • Zhiliang Lu
  • Pan Wang
  • Zhaoli Chen
  • Jie He
Original Article


Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of cancer. To identify novel targets for further study in esophageal squamous cell carcinoma (ESCC), we performed a genome-wide analysis of lncRNA expression in 12 ESCC tumor and normal tissues. Publicly available RNA-seq data were downloaded from the NCBI, GEO, and Co-LncRNA databases, and lncRNA and messenger RNA (mRNA) expression profiles were analyzed. In total, 127 lncRNAs were found to be differentially expressed, with a greater than fourfold change in ESCC tumor tissues compared with normal tissues. Among these lncRNAs, 98 were upregulated and 29 downregulated. Moreover, 1469 network nodes and 1720 connection edges between 119 lncRNAs and 1350 coding genes were integrated into the lncRNA and mRNA co-expression network. Bioinformatic analysis using GO terms revealed that these dysregulated lncRNAs are associated with developmental processes, proteinaceous extracellular matrix, and protein binding activity, with ECM-receptor interaction and the PI3K-Akt signaling pathway enrichment. Lastly, qRT-PCR results verified two significantly upregulated lncRNAs and three significantly downregulated lncRNAs in 50 pairs of ESCC tissues and adjacent normal tissues. These results reveal the landscape of ESCC-associated lncRNAs and co-expression networks, providing important insight regarding the lncRNAs involved in ESCC.


Long non-coding RNA lncRNA Esophageal squamous cell carcinoma ESCC Co-expression network 


Compliance with ethical standards

Samples were obtained with informed consent, and the study was approved by the medical ethics committee of the National Cancer Center/Cancer Hospital.


The work was supported by National Natural Science Foundation of China (81301851, U1302223), The National Key Basic Research Development (973) Plan (2014CB542006) and PUMC Youth Fund (33320140169).

Supplementary material

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Copyright information

© International Society of Oncology and BioMarkers (ISOBM) 2016

Authors and Affiliations

  1. 1.Department of Thoracic Surgery, National Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
  2. 2.Department of Oncologythe First Hospital of Shanxi Medical UniversityTaiyuanChina

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