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.