title: Systemic transcriptome analysis of hepatocellular carcinoma.
abstract: Liver cancer is one of the most common malignant tumors, and most of which is hepatocellular carcinoma (HCC). We aim to study the characteristic changes of numerous genes and their roles in HCC through systematical analysis of the characteristics of expression spectrum of HCC. Firstly, we made systematic clustering of the HCC samples according to the RNAseq data from TCGA (The Cancer Genome Atlas) and newly classified HCC. Then the characteristic genes in different molecular subtypes were found out and further analyzed combing with methylation and SNP 6.0 chip. Finally, these genes were subjected to do functional annotation and abnormal signaling pathways of HCC in various molecular subtypes and were screened out. There were 3843 differential genes screened; among which, 689 genes were enriched into 13 KEGG-related pathways, and the expression of 27 and 924 genes showed positive and negative correlation to methylation level, respectively, while the expression of 43 genes showed positive correlation to variation level of copy number. The methylation degree of ZSCAN18 may be considered as a marker for prognosis evaluation, and ABHD6 could be a potential anti-oncogene.
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou, 310003, China.
authors.forename: Cheng-Bo
authors.initials: CB
authors.lastname: Yu
authors.affiliation: Department of Hepatology, the Fourth People's Hospital of Huai'an, Huai'an, China.
authors.forename: Li-Yao
authors.initials: LY
authors.lastname: Zhu
authors.affiliation: Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
authors.forename: Yu-Gang
authors.initials: YG
authors.lastname: Wang
authors.affiliation: Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071, China.
authors.forename: Fen
authors.initials: F
authors.lastname: Li
authors.affiliation: Division of Gastrointestinal Surgery, Department of General Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an, China. yllzxy@163.com.
authors.forename: Xiao-Yu
authors.initials: XY
authors.lastname: Zhang
authors.affiliation: Department of Gastroenterology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China. daiweijie_yy@163.com.
authors.forename: Wei-Jie
authors.initials: WJ
authors.lastname: Dai
mesh_terms: D014408:Biomarkers, Tumor; D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000401:mortality; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018628:Gene Dosage; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000401:mortality; D058977:Molecular Sequence Annotation; D011379:Prognosis; D059467:Transcriptome
chemical_list: D014408:Biomarkers, Tumor
keywords: ABHD6; Hepatocellular carcinoma; Molecular classification; TCGA; ZSCAN18