title: NGS-based transcriptome profiling reveals biomarkers for companion diagnostics of the TGF-β receptor blocker galunisertib in HCC.
abstract: Transforming growth factor-beta (TGF-β) signaling has gained extensive interest in hepatocellular carcinoma (HCC). The small molecule kinase inhibitor galunisertib, targeting the TGF-β receptor I (TGF-βRI), blocks HCC progression in preclinical models and shows promising effects in ongoing clinical trials. As the drug is not similarly effective in all patients, this study was aimed at identifying new companion diagnostics biomarkers for patient stratification. Next-generation sequencing-based massive analysis of cDNA ends was used to investigate the transcriptome of an invasive HCC cell line responses to TGF-β1 and galunisertib. These identified mRNA were validated in 78 frozen HCC samples and in 26 ex-vivo HCC tissues treated in culture with galunisertib. Respective protein levels in patients blood were measured by enzyme-linked immunosorbent assay. SKIL, PMEPA1 ANGPTL4, SNAI1, Il11 and c4orf26 were strongly upregulated by TGF-β1 and downregulated by galunisertib in different HCC cell lines. In the 78 HCC samples, only SKIL and PMEPA1 (P<0.001) were correlated with endogenous TGF-β1. In ex-vivo samples, SKIL and PMEPA1 were strongly downregulated (P<0.001), and correlated (P<0.001) with endogenous TGF-β1. SKIL and PMEPA1 mRNA expression in tumor tissues was significantly increased compared with controls and not correlated with protein levels in the blood of paired HCC patients. SKIL and PMEPA1 mRNA levels were positively correlated with TGF-β1 mRNA concentrations in HCC tissues and strongly downregulated by galunisertib. The target genes identified here may serve as biomarkers for the stratification of HCC patients undergoing treatment with galunisertib.
authors.affiliation: National Institute of Gastroenterology, IRCCS 'S. De Bellis', Bari, Italy.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Cao
authors.affiliation: GenXPro GmbH, Frankfurt, Germany.
authors.forename: Rahul
authors.initials: R
authors.lastname: Agarwal
authors.affiliation: National Institute of Gastroenterology, IRCCS 'S. De Bellis', Bari, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Dituri
authors.affiliation: Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Lupo
authors.affiliation: Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Trerotoli
authors.affiliation: National Institute of Gastroenterology, IRCCS 'S. De Bellis', Bari, Italy.
authors.forename: Serena
authors.initials: S
authors.lastname: Mancarella
authors.affiliation: GenXPro GmbH, Frankfurt, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Winter
authors.affiliation: National Institute of Gastroenterology, IRCCS 'S. De Bellis', Bari, Italy.
authors.forename: Gianluigi
authors.initials: G
authors.lastname: Giannelli
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics; D006528:Carcinoma, Hepatocellular / Q000188:drug therapy* / Q000235:genetics*; D045744:Cell Line, Tumor; D015536:Down-Regulation / Q000187:drug effects / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D056945:Hep G2 Cells; D006801:Humans; D008113:Liver Neoplasms / Q000188:drug therapy* / Q000235:genetics*; D008565:Membrane Proteins / Q000235:genetics; D011518:Proto-Oncogene Proteins / Q000235:genetics; D011720:Pyrazoles / Q000494:pharmacology*; D011804:Quinolines / Q000494:pharmacology*; D012333:RNA, Messenger / Q000235:genetics; D018125:Receptors, Transforming Growth Factor beta / Q000235:genetics*; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics*; D053773:Transforming Growth Factor beta1 / Q000378:metabolism; D015854:Up-Regulation / Q000187:drug effects / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; D008565:Membrane Proteins; D011518:Proto-Oncogene Proteins; D011720:Pyrazoles; D011804:Quinolines; D012333:RNA, Messenger; D018125:Receptors, Transforming Growth Factor beta; D053773:Transforming Growth Factor beta1; C557799:LY-2157299