Abstract
Objective
To characterize the transcriptome profile of hepatocellular carcinoma (HCC) HepG2 cells treated with peptide 9R-P201 for further functional verification and HCC drug development.
Results
1557 mRNAs (1125 upregulated and 432 downregulated) and 881 lncRNAs (640 upregulated and 241 downregulated) with significant differential expression were identified using RNA-seq. The qRT-PCR results showed that the differential expression of several mRNAs and lncRNAs coincided with the RNA-seq results. Differentially expressed mRNAs and lncRNAs presented a significant difference in genomic characteristics but no preference under 9R-P201 treatment compared with control. The GO and KEGG functional enrichment analyses showed that differentially expressed mRNAs and lncRNAs remarkably enriched in cancer-related biological processes and signaling pathways. Finally, we screened out 33 TFs, 273 lncRNAs and 94 target genes with high degree interaction which were remarkably associated with the tumorigenesis and progression of cancers using betweenness centrality analysis.
Conclusion
These findings offer novel insights into the mechanism of 9R-P201 in HepG2 cells and provide new opportunities for the future 9R-P201-based drug development and the treatment of hepatocellular carcinoma.
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Acknowledgements
This work was financially supported by the Program of the Fundamental Research Funds for the Central Universities of China (2682016YXZT04) and National Natural Science Foundation of China (No. 31200999).
Supporting information
Supplementary Table 1—The qRT-PCR primers of related genes and lncRNAs.
Supplementary Table 2—Differentially expressed mRNAs in Treatment vs. Control.
Supplementary Table 3—Differentially expressed lncRNAs in Treatment vs. Control.
Supplementary Table 4—The functinal enrichment results of differentially expressed lncRNAs.
Supplementary Table 5—The functinal enrichment results of differentially expressed mRNAs.
Supplementary Table 6—The transcription factor binding site analysis of differentially expressed lncRNAs.
Supplementary Table 7—The regulation and interaction relationship of differentially expressed lncRNAs.
Supplementary Table 8—The mutual interaction relationship of differentially expressed mRNAs.
Supplementary Fig. 1—Statistical analysis of clean reads from the control and treatment group.
Supplementary Fig. 2—The screening of the differentially expressed mRNAs and lncRNAs.
Supplementary Fig. 3—Comparative characteristics analysis of differentially expressed mRNAs and lncRNAs.
Supplementary Fig. 4—Comparative characteristics analysis of the all mRNAs and lncRNAs detected in transcriptome sequencing.
Supplementary Fig. 5—The GO function and KEGG pathway annotation analysis of differentially expressed mRNAs and lncRNAs target genes.
Supplementary Fig. 6—Differentially expressed mRNAs were significantly enriched in GO terms and KEGG signaling pathways closely related to cancer.
Supplementary Fig. 7—Cancer-related GO function and KEGG signaling pathway enrichment analysis of differentially expressed mRNAs and lncRNAs.
Supplementary Fig. 8—The regulatory network of TFs-lncRNAs-target genes.
Supplementary Fig. 9—The mutual interaction network of differentially expressed mRNAs.
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Liu, W., Ding, R., Zhang, Y. et al. Transcriptome profiling analysis of differentially expressed mRNAs and lncRNAs in HepG2 cells treated with peptide 9R-P201. Biotechnol Lett 39, 1639–1647 (2017). https://doi.org/10.1007/s10529-017-2407-1
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DOI: https://doi.org/10.1007/s10529-017-2407-1