Differential Analysis of lncRNA, miRNA and mRNA Expression Profiles and the Prognostic Value of lncRNA in Esophageal Cancer

  • Hongtao LiuEmail author
  • Qing Zhang
  • Qianqian Lou
  • Xin Zhang
  • Yunxia Cui
  • Panpan Wang
  • Fan Yang
  • Fan Wu
  • Jing Wang
  • Tianli FanEmail author
  • Shenglei LiEmail author
Original Article


Integrative central axis of lncRNA-miRNA-mRNA plays pivotal roles in tumor development and progression. However, the regulatory role of lncRNA-miRNA-mRNA in esophageal cancer remains elusive. TCGA database was utilized to investigate the differential expression of lncRNA, miRNA and mRNA in esophageal cancer (ESCA) and normal esophageal tissues, and GEO database was used to further validate the expression profile of key genes. Differential lncRNAs in TCGA database were submitted to Starbase, and lncRNAs related to overall survival were analyzed using Kaplan-Meier and log-rank test. We found 145 lncRNAs, 112 miRNAs and 2000 protein coding mRNAs were differentially expressed in ESCA samples, which were tightly involved in chromosome segregation, extracellular matrix assembly by GO assay, and KEGG assay revealed the correlation of differentially expressed genes with cell cycle, apoptosis and cGMP-PKG signaling pathway. Furthermore, there were 291 nodes in ceRNA network, which consisted of 40 lncRNAs, 28 miRNAs and 233 mRNAs, and formed 677 relations. Furthermore, 6 of 10 lncRNAs in TCGA database were consistent with GEO database, and expressions of 10 mRNAs in TCGA database all exhibited the same tendency with GEO database. Notably, we found 8 lncRNAs (WDFY3-AS2, CASC8, UGDH-AS1, RAP2C-AS1, AC007128.1, AC016205.1, AC092803.2 and AC079949.2) were correlated with overall survival of the patients with ESCA. The key differentially expressed genes participate in the development and progression of ESCA, and thus the elucidation of functions of lncRNA-miRNA-mRNA will provide new novel therapeutic target for the patients with ESCA.


Long chain non-coding RNA MicroRNA Messagers RNA Differential expression ceRNA Esophageal cancer 



This work was supported by the Natural Science Foundation of Henan Province (No. 182300410377), the Key scientific research projects of Henan higher education institutions (No.17A180016), the National Natural Science Foundation of China (No.81272691, 30600006).

Compliance with Ethical Standards

Declaration of Conflicting Interests

The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Supplementary material

12253_2019_655_MOESM1_ESM.jpg (3.7 mb)
Supplementary Figure 1 Heatmap analysis for differential expressions of top 30 of lncRNA, miRNA and mRNA in ESCC and normal esophageal tissues. A: lncRNAs were displayed using heatmap in ESCC and normal esophageal tissues; B: miRNAs were displayed using heatmap in ESCC and normal esophageal tissues; C: protein coding mRNAs were displayed using heatmap in ESCC and normal esophageal tissues. X axis represents the samples, and Y axis denotes differential expressions of lncRNAs, miRNAs and mRNAs. (JPG 3831 kb)
12253_2019_655_MOESM2_ESM.jpg (1.3 mb)
Supplementary Figure 2 Prognostic investigation of a total of 15 of high nodes regarding lncRNAs, miRNAs and mRNAs. LncRNAs, miRNAs and mRNAs were submitted to Starbase online software as described in online manufacture’s instructions. (JPG 1280 kb)
12253_2019_655_MOESM3_ESM.jpg (844 kb)
Supplementary Figure 3 Prognostic assay of the 10 mRNAs in ESCA. The 10 mRNAs were submitted to Starbase online software as described in online manufacture’s instructions. (JPG 844 kb)
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Supplementary Table 1 (DOCX 17 kb)
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Supplementary Table 2 (DOCX 16 kb)
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Supplementary Table 3 (DOCX 17 kb)
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Supplementary Table 4 (DOCX 16 kb)
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Supplementary Table 5 (DOCX 16 kb)


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Copyright information

© Arányi Lajos Foundation 2019

Authors and Affiliations

  1. 1.College of Life SciencesZhengzhou UniversityZhengzhouPeople’s Republic of China
  2. 2.Department of Pharmacology, School of Basic MedicineZhengzhou UniversityZhengzhouChina
  3. 3.Department of PathologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina

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