Clinical and Translational Research
Copyright ©The Author(s) 2022. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastrointest Oncol. Jul 15, 2022; 14(7): 1265-1280
Published online Jul 15, 2022. doi: 10.4251/wjgo.v14.i7.1265
Differences of core genes in liver fibrosis and hepatocellular carcinoma: Evidence from integrated bioinformatics and immunohistochemical analysis
Yue Li, Shou-Li Yuan, Jing-Ya Yin, Kun Yang, Xin-Gang Zhou, Wen Xie, Qi Wang
Yue Li, Kun Yang, Xin-Gang Zhou, Department of Pathology, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
Yue Li, Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
Shou-Li Yuan, Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing 100101, China
Jing-Ya Yin, Wen Xie, Qi Wang, Center of Liver Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
Author contributions: Li Y and Yuan SL contributed equally to this work; Wang Q and Xie W designed the research and were co-corresponding authors; Yuan SL, Li Y, Yin JY, Yang K and Zhou XG performed the experiments; Yuan SL and Li Y analyzed the data; Yuan SL, Li Y and Wang Q wrote the manuscript; Yuan SL provided vital reagents and analytical tools; all authors read and approved the final manuscript.
Supported by the Beijing Natural Science Foundation, No. 7222097; Beijing Hospitals Authority the Digestive Medical Coordinated Development Center, No. XXZ0401; National Natural Science Foundation of China, No. 82000555 and No. 81900547; and Beijing Municipal Science and Technology Commission, No. D171100003117005.
Institutional review board statement: The study protocol conforms to the ethical guidelines of the 1975 Declaration of Helsinki as reflected in a priori approval by the Ethics Committee of Beijing Ditan Hospital No. 2021-034-01.
Informed consent statement: Patients were not required to give informed consent to the study because the analysis used anonymous clinical data and liver tissue samples.
Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.
Data sharing statement: Publicly available datasets were analyzed in this study, which can be found here: GSE14323, GSE36411 and GSE89377. Technical appendix, statistical code, and data set available from the corresponding author at wangqidl04@ccmu.edu.cn. No additional data are available.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/
Corresponding author: Qi Wang, MD, PhD, Reader (Associate Professor), Center of Liver Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 East Jingshun Street, Chaoyang District, Beijing 100015, China. wangqidl04@ccmu.edu.cn
Received: January 25, 2022
Peer-review started: January 25, 2022
First decision: May 9, 2022
Revised: May 18, 2022
Accepted: June 26, 2022
Article in press: June 26, 2022
Published online: July 15, 2022
Abstract
BACKGROUND

Liver fibrosis and hepatocellular carcinoma (HCC) are common adverse consequences of chronic liver injury. The interaction of various risk factors may cause them to happen. Identification of specific biomarkers is of great significance for understanding the occurrence, development mechanisms, and determining the novel tools for diagnosis and treatment of both liver fibrosis and HCC.

AIM

To identify liver fibrosis-related core genes, we analyzed the differential expression pattern of core genes in liver fibrosis and HCC.

METHODS

Gene expression profiles of three datasets, GSE14323, GSE36411, and GSE89377, obtained from the Gene Expression Omnibus (GEO) database, were analyzed, and differentially expressed genes (DEGs) between patients with liver cirrhosis and healthy controls were identified by screening via R software packages and online tool for Venn diagrams. The WebGestalt online tool was used to identify DEGs enriched in biological processes, molecular functions, cellular components, and Kyoto Encyclopedia of Genes and Genomes pathways. The protein–protein interactions of DEGs were visualized using Cytoscape with STRING. Next, the expression pattern of core genes was analyzed using Western blot and immunohistochemistry in a carbon tetrachloride (CCl4)-induced liver cirrhosis mouse model and in patient liver samples. Finally, Kaplan-Meier curves were constructed using the Kaplan-Meier plotter online server.

RESULTS

Forty-five DEGs (43 upregulated and 2 downregulated genes) associated with liver cirrhosis were identified from three GEO datasets. Ten hub genes were identified, which were upregulated in liver cirrhosis. Western blot and immunohistochemical analyses of the three core genes, decorin (DCN), dermatopontin (DPT), and SRY-box transcription factor 9 (SOX9), revealed that they were highly expressed in the CCl4-induced liver cirrhosis mouse model. The expression levels of DCN and SOX 9 were positively correlated with the degree of fibrosis, and SOX 9 level in HCC patients was significantly higher than that in fibrosis patients. However, high expression of DPT was observed only in patients with liver fibrosis, and its expression in HCC was low. The gene expression profiling interactive analysis server (GEPIA) showed that SOX9 was significantly upregulated whereas DCN and DPT were significantly downregulated in patients with HCC. In addition, the Kaplan-Meier curves showed that HCC patients with higher SOX9 expression had significantly lower 5-year survival rate, while patients with higher expression of DCN or DPT had significantly higher 5-year survival rates.

CONCLUSION

The expression levels of DCN, DPT, and SOX9 were positively correlated with the degree of liver fibrosis but showed different correlations with the 5-year survival rates of HCC patients.

Keywords: Liver cirrhosis, Hepatocellular carcinoma, Bioinformatical analysis, Decorin, Dermatopontin, SRY-box transcription factor 9

Core Tip: GSE14323, GSE36411, and GSE89377 are available from the Gene Expression Omnibus database. Forty-five differentially expressed genes and 10 hub genes were identified between cirrhotic and healthy livers. quantitative polymerase chain reaction, Western blot, and immunohistochemical analyses showed that decorin (DCN), dermatopontin (DPT), and SRY-box transcription factor 9 (SOX9) were highly expressed in the CCl4-induced cirrhotic mouse model. The expression level of SOX9 was also significantly increased in HCC patients,and was associated with the fibrosis stage.. However, overexpression of DPT was only observed in patients with liver fibrosis. The Kaplan-Meier curves showed that HCC patients with higher SOX9 expression had significantly lower 5-year survival rate, while patients with higher expression of DCN or DPT had higher 5-year survival rates.