Subscribe to RSS
Shared Genes and Molecular Mechanisms between Nonalcoholic Fatty Liver Disease and Hepatocellular Carcinoma Established by WGCNA AnalysisFunding This research was funded by Henan Province Characteristic Backbone Discipline TCM Discipline Construction Project (STG-ZYXKY-2020019) and Henan Province Characteristic Backbone Discipline Chinese Medicine Second Batch Discipline Construction Project (STG-ZYX03-202126).
Background Hepatocellular carcinoma (HCC) is one of the leading causes of death from cancer worldwide. The histopathological features, risk factors, and prognosis of HCC caused by nonalcoholic fatty liver disease (NAFLD) appear to be significantly different from those of HCC caused by other etiologies of liver disease.
Objective This article explores the shared gene and molecular mechanism between NAFLD and HCC through bioinformatics technologies such as weighted gene co-expression network analysis (WGCNA), so as to provide a reference for comprehensive understanding and treatment of HCC caused by NAFLD.
Methods NAFLD complementary deoxyribonucleic acid microarrays (GSE185051) from the Gene Expression Omnibus database and HCC ribonucleic acid (RNA)-sequencing data (RNA-seq data) from The Cancer Genome Atlas database were used to analyze the differentially expressed genes (DEGs) between NAFLD and HCC. Then, the clinical traits and DEGs in the two disease data sets were analyzed by WGCNA to obtain W-DEGs, and cross-W-DEGs were obtained by their intersection. We performed subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichment analyses of the cross-W-DEGs and established protein–protein interaction networks. Then, we identified the hub genes in them by Cytoscape and screened out the final candidate genes. Finally, we validated candidate genes by gene expression, survival, and immunohistochemical analyses.
Results The GO analysis of 79 cross-W-DEGs showed they were related mainly to RNA polymerase II (RNAP II) and its upstream transcription factors. KEGG analysis revealed that they were enriched predominantly in inflammation-related pathways (tumor necrosis factor and interleukin-17). Four candidate genes (JUNB, DUSP1, NR4A1, and FOSB) were finally screened out from the cross-W-DEGs.
Conclusion JUNB, DUSP1, NR4A1, and FOSB inhibit NAFLD and HCC development and progression. Thus, they can serve as potential useful biomarkers for predicting and treating NAFLD progression to HCC.
KeywordsWGCNA - nonalcoholic fatty liver disease - hepatocellular carcinoma - genes - bioinformatics
Ethics Approval and Consent to Participate
Consent for Publication
Availability of Data and Material
All the basic data involved in the analysis of this paper have been uploaded as Supplementary Files (SF), including the GSE185051 data set and the TCGA database gene expression matrix (SF 1, 2), and their differential gene matrix (SF 3, 4). The clinical phenotype information of the samples corresponding to the gene matrix (SF 5, 6) and the cross-W-DEGs of NAFLD and HCC (SF 7) were also included. KEGG, GO, PPI, and CytoHubba analysis results of cross-W-DEGs (SF 8, 9, 10, 11), the expression level validation results (SF 12, 13, 14), and the survival analysis results (SF 15, 16, 17, 18) of the candidate genes were also uploaded in the Supplementary Files.
Z.X. realized the conception, data collection, and analysis in the article. H.J. performed the writing and editing. The remaining authors provided editing and writing assistance. All authors contributed to this article and read the submitted final version.
# These authors contributed equally to this work.
Article published online:
10 July 2023
© 2023. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/)
Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany
- 1 Llovet JM, Kelley RK, Villanueva A. et al. Hepatocellular carcinoma. Nat Rev Dis Primers 2021; 7 (01) 6
- 2 Sung H, Ferlay J, Siegel RL. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2021; 71 (03) 209-249
- 3 Güzelcan EA, Baxendale IR, Cetin-Atalay R, Baumann M. Synthesis of new derivatives of boehmeriasin A and their biological evaluation in liver cancer. Eur J Med Chem 2019; 166: 243-255
- 4 Powell EE, Wong VW, Rinella M. Non-alcoholic fatty liver disease. Lancet 2021; 397 (10290): 2212-2224
- 5 Bellentani S. The epidemiology of non-alcoholic fatty liver disease. Liver Int 2017; 37 (Suppl. 01) 81-84
- 6 Petrelli F, Manara M, Colombo S. et al. Hepatocellular carcinoma in patients with nonalcoholic fatty liver disease: a systematic review and meta-analysis: HCC and Steatosis or Steatohepatitis. Neoplasia 2022; 30: 100809
- 7 Orci LA, Sanduzzi-Zamparelli M, Caballol B. et al. Incidence of hepatocellular carcinoma in patients with nonalcoholic fatty liver disease: a systematic review, meta-analysis, and meta-regression. Clin Gastroenterol Hepatol 2022; 20 (02) 283-292.e10
- 8 Wu J. Utilization of animal models to investigate nonalcoholic steatohepatitis-associated hepatocellular carcinoma. Oncotarget 2016; 7 (27) 42762-42776
- 9 Cai C, Song X, Yu C. Identification of genes in hepatocellular carcinoma induced by non-alcoholic fatty liver disease. Cancer Biomark 2020; 29 (01) 69-78
- 10 Ye J, Li TS, Xu G. et al. JCAD promotes progression of nonalcoholic steatohepatitis to liver cancer by inhibiting LATS2 kinase activity. Cancer Res 2017; 77 (19) 5287-5300
- 11 Zhou F, Zhou J, Wang W. et al. Unexpected rapid increase in the burden of NAFLD in China from 2008 to 2018: a systematic review and meta-analysis. Hepatology 2019; 70 (04) 1119-1133
- 12 Li J, Zou B, Yeo YH. et al. Prevalence, incidence, and outcome of non-alcoholic fatty liver disease in Asia, 1999-2019: a systematic review and meta-analysis. Lancet Gastroenterol Hepatol 2019; 4 (05) 389-398
- 13 Huang DQ, El-Serag HB, Loomba R. Global epidemiology of NAFLD-related HCC: trends, predictions, risk factors and prevention. Nat Rev Gastroenterol Hepatol 2021; 18 (04) 223-238
- 14 Stine JG, Wentworth BJ, Zimmet A. et al. Systematic review with meta-analysis: risk of hepatocellular carcinoma in non-alcoholic steatohepatitis without cirrhosis compared to other liver diseases. Aliment Pharmacol Ther 2018; 48 (07) 696-703
- 15 Hu P, Wang B, Chen T. et al. RNA polymerase II subunit 3 regulates vesicular, overexpressed in cancer, prosurvival protein 1 expression to promote hepatocellular carcinoma. J Int Med Res 2021; 49 (04) 300060521990512
- 16 Zhong L, Yang S, Jia Y, Lei K. Inhibition of cyclin-dependent kinase 7 suppresses human hepatocellular carcinoma by inducing apoptosis. J Cell Biochem 2018; 119 (12) 9742-9751
- 17 Katsarou A, Moustakas II, Pyrina I, Lembessis P, Koutsilieris M, Chatzigeorgiou A. Metabolic inflammation as an instigator of fibrosis during non-alcoholic fatty liver disease. World J Gastroenterol 2020; 26 (17) 1993-2011
- 18 Nati M, Haddad D, Birkenfeld AL, Koch CA, Chavakis T, Chatzigeorgiou A. The role of immune cells in metabolism-related liver inflammation and development of non-alcoholic steatohepatitis (NASH). Rev Endocr Metab Disord 2016; 17 (01) 29-39
- 19 Yang YM, Kim SY, Seki E. Inflammation and liver cancer: molecular mechanisms and therapeutic targets. Semin Liver Dis 2019; 39 (01) 26-42
- 20 Park EJ, Lee JH, Yu GY. et al. Dietary and genetic obesity promote liver inflammation and tumorigenesis by enhancing IL-6 and TNF expression. Cell 2010; 140 (02) 197-208
- 21 Li N, Yamamoto G, Fuji H, Kisseleva T. Interleukin-17 in liver disease pathogenesis. Semin Liver Dis 2021; 41 (04) 507-515
- 22 Wu H, Xu X, Zheng A. et al. TNF-α-induce protein 8-like 1 inhibits hepatic steatosis, inflammation, and fibrosis by suppressing polyubiquitination of apoptosis signal-regulating kinase 1. Hepatology 2021; 74 (03) 1251-1270
- 23 Serhal R, Hilal G, Boutros G. et al. Nonalcoholic steatohepatitis: involvement of the telomerase and proinflammatory mediators. BioMed Res Int 2015; 2015: 850246
- 24 Shen J, Zhang Y, Yu H. et al. Role of DUSP1/MKP1 in tumorigenesis, tumor progression and therapy. Cancer Med 2016; 5 (08) 2061-2068
- 25 Delire B, Stärkel P. The Ras/MAPK pathway and hepatocarcinoma: pathogenesis and therapeutic implications. Eur J Clin Invest 2015; 45 (06) 609-623
- 26 Hao PP, Li H, Lee MJ. et al. Disruption of a regulatory loop between DUSP1 and p53 contributes to hepatocellular carcinoma development and progression. J Hepatol 2015; 62 (06) 1278-1286
- 27 Lopez-Yus M, Lorente-Cebrian S, Del Moral-Bergos R. et al. Identification of novel targets in adipose tissue involved in non-alcoholic fatty liver disease progression. FASEB J 2022; 36 (08) e22429
- 28 Yan P, Zhou B, Ma Y. et al. Tracking the important role of JUNB in hepatocellular carcinoma by single-cell sequencing analysis. Oncol Lett 2020; 19 (02) 1478-1486
- 29 Mechta-Grigoriou F, Gerald D, Yaniv M. The mammalian Jun proteins: redundancy and specificity. Oncogene 2001; 20 (19) 2378-2389
- 30 Wutschka J, Kast B, Sator-Schmitt M. et al. JUNB suppresses distant metastasis by influencing the initial metastatic stage. Clin Exp Metastasis 2021; 38 (04) 411-423
- 31 Shaulian E, Karin M. AP-1 as a regulator of cell life and death. Nat Cell Biol 2002; 4 (05) E131-E136
- 32 Jin JY, Ke H, Hall RP, Zhang JY. c-Jun promotes whereas JunB inhibits epidermal neoplasia. [published correction appears in J Invest Dermatol. 2011 Jun;131(6):1388] J Invest Dermatol 2011; 131 (05) 1149-1158
- 33 Guo C, Liu QG, Zhang L, Song T, Yang X. Expression and clinical significance of p53, JunB and KAI1/CD82 in human hepatocellular carcinoma. Hepatobiliary Pancreat Dis Int 2009; 8 (04) 389-396
- 34 Guo C, Liu Q, Zhang L, Yang X, Song T, Yao Y. Double lethal effects of fusion gene of wild-type p53 and JunB on hepatocellular carcinoma cells. J Huazhong Univ Sci Technolog Med Sci 2012; 32 (05) 663-668
- 35 Du J, Fu L, Ji F, Wang C, Liu S, Qiu X. FosB recruits KAT5 to potentiate the growth and metastasis of papillary thyroid cancer in a DPP4-dependent manner. Life Sci 2020; 259: 118374
- 36 Zhang R, Li X, Liu Z, Wang Y, Zhang H, Xu H. EZH2 inhibitors-mediated epigenetic reactivation of FOSB inhibits triple-negative breast cancer progress. Cancer Cell Int 2020; 20: 175
- 37 Ting CH, Lee KY, Wu SM. et al. FOSB–PCDHB13 axis disrupts the microtubule network in non-small cell lung cancer. Cancers (Basel) 2019; 11 (01) 107
- 38 Barrett CS, Millena AC, Khan SA. TGF-β effects on prostate cancer cell migration and invasion require FosB. Prostate 2017; 77 (01) 72-81
- 39 Hu B, Yu M, Ma X. et al. IFNα potentiates anti-PD-1 efficacy by remodeling glucose metabolism in the hepatocellular carcinoma microenvironment. Cancer Discov 2022; 12 (07) 1718-1741
- 40 Papoudou-Bai A, Hatzimichael E, Barbouti A, Kanavaros P. Expression patterns of the activator protein-1 (AP-1) family members in lymphoid neoplasms. Clin Exp Med 2017; 17 (03) 291-304
- 41 Hasenfuss SC, Bakiri L, Thomsen MK, Williams EG, Auwerx J, Wagner EF. Regulation of steatohepatitis and PPARγ signaling by distinct AP-1 dimers. Cell Metab 2014; 19 (01) 84-95
- 42 Safe S, Karki K. The paradoxical roles of orphan nuclear receptor 4A (NR4A) in cancer. Mol Cancer Res 2021; 19 (02) 180-191
- 43 Zhu B, Yang JR, Jia Y. et al. Overexpression of NR4A1 is associated with tumor recurrence and poor survival in non-small-cell lung carcinoma. Oncotarget 2017; 8 (69) 113977-113986
- 44 Lee SO, Jin UH, Kang JH. et al. The orphan nuclear receptor NR4A1 (Nur77) regulates oxidative and endoplasmic reticulum stress in pancreatic cancer cells. Mol Cancer Res 2014; 12 (04) 527-538
- 45 Smith AG, Lim W, Pearen M, Muscat GE, Sturm RA. Regulation of NR4A nuclear receptor expression by oncogenic BRAF in melanoma cells. Pigment Cell Melanoma Res 2011; 24 (03) 551-563
- 46 Guan YF, Huang QL, Ai YL. et al. Nur77-activated lncRNA WFDC21P attenuates hepatocarcinogenesis via modulating glycolysis. Oncogene 2020; 39 (11) 2408-2423
- 47 He L, Yuan L, Yu W. et al. A regulation loop between YAP and NR4A1 balances cell proliferation and apoptosis. Cell Rep 2020; 33 (03) 108284
- 48 Zhao Y, Bruemmer D. NR4A orphan nuclear receptors: transcriptional regulators of gene expression in metabolism and vascular biology. Arterioscler Thromb Vasc Biol 2010; 30 (08) 1535-1541
- 49 Chao LC, Wroblewski K, Zhang Z. et al. Insulin resistance and altered systemic glucose metabolism in mice lacking Nur77. Diabetes 2009; 58 (12) 2788-2796