Abstract
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play vital roles in the tumorigenesis of esophageal squamous cell carcinoma (ESCC). Nevertheless, the mechanism and regulatory network associated with this process remain largely unknown. In this study, we performed a comprehensive analysis of the expression of mRNAs, lncRNAs, and circRNAs by RNA-seq. A total of 3265 mRNAs, 1084 lncRNAs, and 38 circRNAs were found to be differentially expressed. Among these, 269 mRNAs were found to encode transcription factors (TFs). Functional enrichment analysis indicated that the dysregulated TFs are associated with the Hedgehog, Jak-STAT, TGF-beta, and MAPK signaling pathways. Furthermore, we constructed co-expression networks to screen the core lncRNAs and circRNAs involved in the regulation of transcription factors in these four pathways. Finally, we constructed a competing endogenous RNA (ceRNA) network of ESCC based on the abovementioned pathways. Our findings provide important insight into the role of lncRNAs and circRNAs in ESCC; the differentially expressed lncRNAs and circRNAs may represent potential targets for ESCC diagnosis and therapy.
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This work was supported by the National Science Foundation of China (grant number 81972800).
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Supplementary Fig. 1
A hierarchical tree of the GO terms based on their associations. The parameters define up regulated, down regulated or all differentially expressed genes related Go terms. (PNG 498 kb)
Supplementary Fig. 2
Co-expression network of four TF-affecting pathways with their associated lncRNAs and circRNAs in adjacent normal tissues. a. Co-expression network of four TF-affecting pathways with their associated lncRNAs. b. Co-expression network of four TF-affecting pathways with their associated circRNAs. (PNG 1766 kb)
Supplementary Fig. 3
Schematic representation of ceRNA network involved in TGF-beta, Hedgehog and MAPK signaling pathways. a. CeRNA network involved in the TGF-beta signaling pathway. b. CeRNA network involved in the Hedgehog signaling pathway. c. CeRNA network involved in the MAPK signaling pathway. (PNG 1534 kb)
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Shen, JF., Ge, JF., Zheng, SY. et al. Integrative analysis of differential circular RNA and long non-coding RNA profiles and associated competing endogenous RNA networks in esophageal squamous cell carcinoma. Funct Integr Genomics 21, 125–138 (2021). https://doi.org/10.1007/s10142-020-00765-6
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DOI: https://doi.org/10.1007/s10142-020-00765-6