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Identification of the Pathogenic Biomarkers for Hepatocellular Carcinoma Based on RNA-seq Analyses

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Pathology & Oncology Research

Abstract

The purpose of this study was to explore potential biomarkers in the diagnosis of hepatocellular carcinoma (HCC) based on RNA-seq. The microarray data GSE98269 were downloaded from the GEO database, including the miRNA, mRNA and lncRNA expression profiles of 3 HCC tissues and 3 normal liver tissues from 3 HCC patients. The limma package was used to identify the differentially expressed miRNAs (DEMs) and the differentially expressed lncRNAs in HCC tissues compared with normal liver tissues. Database of DAVID, KEGG PATHWAY and Reactome were used to perform the functional and pathway enrichment. Putative targets for DEMs, and the miRNA-gene pairs were predicted via the miRWalk V2.0 database. The protein-protein pairs of DEGs were screened via String software. The expression features of the differentially expressed lncRNAs were analyzed. The regulated network of DEGs and DEMs were constructed, and related genes and miRNAs were detected in the HCC tissues and normal liver samples with Q-PCR. A total of 678 DEGs, 32 DEMs and 411 differential expressed lncRNAs were identified. The DEGs were enriched in 196 GO terms and 79 pathways. 38 negative regulation miRNA-gene pairs and 1205 protein-protein interactions were screened out, and the regulated network was constructed based on them. KNG1, CDK1, EHHADH, CYP3A4, hsa-miR-199a-5p and hsa-miR-455-3p might be biomarkers in the occurrence of HCC.

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Data Availability

The datasets used during the present study are available from the corresponding author upon reasonable request.

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Acknowledgements

We would like to thank all the members of our research group for their enthusiastic participation in this study.

Funding

Tianjin Clinical Research Center for Organ Transplantation (Grant No.15ZXLCSY00070); International Science and Technology Cooperation Program of China (Grant No. 2015DFG31850); National Key Clinical Specialty Construction Project of Organ Transplantation Department (Grant No.2013544); Science and Technology Fund of Tianjin Municipal Health Bureau (Grant No. 2013 KZ034); The study of precisely medical technology in the perioperative period of liver transplantation for liver cancer (Grant No. 17ZXMFSY00040); Spring Buds Project (Grant No. CL201801); General Program of The National Natural Science Foundation of China (Grant No. 81870444); Trial Registration Clinical Trial Registration URL: http://www.chictr.org.cn/showproj.aspx?proj=19662 webcite Trial Registration number: ChiCTR-ROR-17012157.

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Author notes

  1. Wentao Jiang and Li Zhang contributed equally to this work.

Authors and Affiliations

  1. Department of Liver Transplantation, Key Laboratory for Critical Care Medicine of the Ministry of Health, Tianjin Key Laboratory for Organ Transplantation, Tianjin First Center Hospital, 24 Fukang Road, Nankai District, Tianjin, 300192, People’s Republic of China

    Wentao Jiang, Li Zhang, Qingjun Guo, Honghai Wang, Ming Ma, Jisan Sun & Chiyi Chen

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  1. Wentao Jiang
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  2. Li Zhang
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  3. Qingjun Guo
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  4. Honghai Wang
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  7. Chiyi Chen
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Correspondence to Wentao Jiang.

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Jiang, W., Zhang, L., Guo, Q. et al. Identification of the Pathogenic Biomarkers for Hepatocellular Carcinoma Based on RNA-seq Analyses. Pathol. Oncol. Res. 25, 1207–1213 (2019). https://doi.org/10.1007/s12253-019-00596-2

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  • DOI: https://doi.org/10.1007/s12253-019-00596-2

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