title: Extracellular matrix transcriptome dynamics in hepatocellular carcinoma.
abstract: The extracellular matrix undergoes extensive remodeling during hepatocellular carcinoma and functions as a critical component of the tumor microenvironment by providing a substratum for cell adhesion and serving as a reservoir for a variety of cytokines and growth factors. Despite the clinical correlation between ECM deposition and hepatocellular carcinoma progression, it remains unclear how global extracellular matrix gene expression is altered in hepatocellular carcinoma and the molecular pathways that govern this change. Herein, a comprehensive analysis of the extracellular matrix transcriptome using an RNA-sequencing dataset provided by The Cancer Genome Atlas consortium was conducted and indicates substantial differential gene expression of key extracellular matrix collagens, glycoproteins, and proteoglycans in hepatocellular carcinoma. This analysis also reveals alternative expression of extracellular matrix gene transcript variants that could impact biological activity and serves as a framework for exploring the dynamic nature of the extracellular matrix transcriptome in cancer and identifying candidate genes for future exploration.
authors.affiliation: Section of Gastroenterology/Hepatology, Department of Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States; Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, United States; Georgia Regents University Cancer Center, Georgia Regents University, Augusta, GA 30912, United States. Electronic address: mduncan@gru.edu.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Duncan
mesh_terms: D001483:Base Sequence; D006528:Carcinoma, Hepatocellular / Q000378:metabolism*; D019295:Computational Biology; D016326:Extracellular Matrix Proteins / Q000378:metabolism*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics / Q000502:physiology*; D006801:Humans; D008113:Liver Neoplasms / Q000378:metabolism*; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000502:physiology*
chemical_list: D016326:Extracellular Matrix Proteins
keywords: Cancer; Collagen; Glycoprotein; Proteoglycan; RNA-Seq