Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq

Yi Huang; Jianbo Pan; Dunyan Chen; Jiaying Zheng; Funan Qiu; Feng Li; Yanan Wu; Wenbing Wu; Xiaoli Huang; Jiang Qian

doi:10.18632/oncotarget.16415

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Research Papers:

Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq

Yi Huang _, Jianbo Pan, Dunyan Chen, Jiaying Zheng, Funan Qiu, Feng Li, Yanan Wu, Wenbing Wu, Xiaoli Huang and Jiang Qian

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Oncotarget. 2017; 8:35973-35983. https://doi.org/10.18632/oncotarget.16415

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Abstract

Yi Huang1,2,*, Jianbo Pan3,*, Dunyan Chen1,2, Jiaying Zheng1,2, Funan Qiu1,4, Feng Li2,5, Yanan Wu1,2, Wenbing Wu1,2, Xiaoli Huang1,2, Jiang Qian3,6

1Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, Fujian 350001, China

2Provincial Clinical College, Fujian Medical University, Fuzhou, Fujian 350001, China

3Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA

4Department of Hepatobiliary Surgery, Fujian Provincial Hospital, Fuzhou, Fujian 350001, China

5Department of Pathology, Fujian Provincial Hospital, Fuzhou, Fujian 350001, China

6The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA

*These authors contributed equally to this work

Correspondence to:

Yi Huang, email: [email protected]

Jiang Qian, email: [email protected]

Keywords: hepatocellular carcinoma, poorly differentiated, transcriptome sequencing, differentially expressed genes, carcinogenesis

Received: February 07, 2017 Accepted: March 12, 2017 Published: March 21, 2017

ABSTRACT

Poorly differentiated (PD) hepatocellular carcinoma (HCC) has a worse prognosis compared to moderately differentiated (MD) and well differentiated (WD) HCC. We aimed to identify differentially expressed genes (DEGs) to explore the mechanism of PD HCC. Transcriptome sequencing was performed on tumor and adjacent non-tumorous tissues of PD, MD and WD HCC patients (3 for each group). DEGs were thus identified and functionally analyzed. Further RT-PCR was performed to validate DEGs specific for PD HCC in 47 pairs of samples (15 for PD, 18 for MD, 14 for WD). A total of 681 PD DEGs were detected, including 368 up-regulated and 313 down-regulated genes. Less DEGs were found for MD and especially for WD HCC. Through bioinformatics analysis, PD HCC DEGs were enriched in liver tissue and liver cancer cells, and in biological process and pathway including metabolism, cell cycle, translation and blood coagulation. Potential drugs and genetic perturbations were found to reverse the cancer condition. The RT-PCR results showed consistency with RNA-seq in the validation of 4 DEGs specific for PD HCC. This study detected and validated DEGs of PD HCC, which provides useful information on molecular mechanism of PD HCC for development of new biomarkers, therapeutic targets and drugs.

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Research Papers:

Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq

Abstract