title: Transcriptome and proteome of human hepatocellular carcinoma reveal shared metastatic pathways with significant genes.
abstract: Previously isolated pathways screened from individual genes were investigated at either the transcriptional or translational level; however, the consistency between the pathways screened at the gene expression levels was obscure in metastatic human hepatocellular carcinoma (HCC). To elucidate this question, we performed a transcriptomic (16,353 genes) and proteomic (7861 proteins) analysis simultaneously on six metastatic HCC cell lines against two nonmetastatic HCC cell lines, with all HBV traceable and close genetic-backgrounds for a comparative study. The quantitative and integrated results showed that significant genes were screened differentially with 351 transcripts from the transcriptome and 304 proteins from the proteome, with limited overlapping genes (7%). However, we discovered that these discrete 351 transcripts and 304 proteins screened share extrusive significant-pathways/networks with a 77% overlap, including active TGF-β, RAS, NFκB, and Wnt, and inactive HNF4A, which are responsible for HCC metastasis. We conclude that the discrete, but significant genes predicted by either ome play intrinsically important roles in the linkage of responsible pathways shared by both omes in HCC metastasis.
authors: Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P. R. China.|Department of Chemistry, Fudan University, Shanghai, P. R. China.
authors: Huali
authors: H
authors: Shen
authors: Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P. R. China.
authors: Fan
authors: F
authors: Zhong
authors: Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P. R. China.
authors: Yang
authors: Y
authors: Zhang
authors: Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P. R. China.
authors: Hongxiu
authors: H
authors: Yu
authors: Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P. R. China.|Zhongshan Hospital, Fudan University, Shanghai, P. R. China.
authors: Yinkun
authors: Y
authors: Liu
authors: Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P. R. China.|Zhongshan Hospital, Fudan University, Shanghai, P. R. China.
authors: Lunxiu
authors: L
authors: Qin
authors: Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P. R. China.|State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, P. R. China.
authors: Fuchu
authors: F
authors: He
authors: Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P. R. China.|Zhongshan Hospital, Fudan University, Shanghai, P. R. China.
authors: Zhaoyou
authors: Z
authors: Tang
authors: Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, P. R. China.|Department of Chemistry, Fudan University, Shanghai, P. R. China.|Children Hospital, Fudan University, Shanghai, P. R. China.
authors: Pengyuan
authors: P
authors: Yang
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D058750:Epithelial-Mesenchymal Transition / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D020543:Proteome / Q000032:analysis* / Q000378:metabolism; D016212:Transforming Growth Factor beta / Q000235:genetics / Q000378:metabolism; D060449:Wnt Signaling Pathway / Q000235:genetics; D018631:ras Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D020543:Proteome; D016212:Transforming Growth Factor beta; D018631:ras Proteins
keywords: Animal proteomics; Hepatocellular carcinoma; Metastasis; Pathway; Transcriptome