Abstract Background and Aims Numerous studies in hepatocellular carcinoma (HCC) have proposed tissue-based gene signatures for individualized prognostic assessments. In this study, we aim to develop the HCC circulating tumor cell (CTC) mRNA Scoring System and the HCC-CTC Risk Score (RS) panel to translate tissue-based mRNA signatures into a liquid biopsy setting for non-invasive HCC prognostication. Methods We developed the HCC CTC mRNA Scoring System by combining the NanoVelcro CTC Assay for enriching HCC CTCs and the NanoString nCounter platform for quantifying the HCC-CTC RS panel in enriched HCC CTCs. The prognostic role of HCC-CTC RS was assessed in the Cancer Genome Atlas (TCGA) HCC cohort (n=362) and validated in an independent CTC cohort (n=40). Results The HCC-CTC RS panel was developed from 8 HCC tissue-based prognostic gene signatures. Through our integrated data analysis framework, the top 10 prognostic genes highly expressed in HCC cells and lowly expressed in white blood cells were selected as the HCC-CTC RS panel. The panel accurately discriminated overall survival in TCGA HCC cohort (hazard ratio [HR]: 2.01, 95% confidence intervals [CI]: 1.39-2.91). In addition, the combined use of Scoring System and panel successfully distinguished artificial blood samples spiked with an aggressive HCC cell type, SNU-387, from those spiked with PLC/PRF/5 cells (P=0.02). Finally, the prognostic value of HCC-CTC RS was further validated in the CTC cohort (HR: 8.48, 95% CI: 1.89-38.03) by multivariable analysis. Conclusions Our pilot study demonstrates a novel interdisciplinary approach to translate tissue-based gene signatures into a liquid biopsy setting. This non-invasive approach will allow real-time disease profiling and dynamical prognostication of HCC. Citation Format: Yi-Te Lee, Na Sun, Minhyung Kim, Jasmine J. Wang, Benjamin V. Tran, Ryan Y. Zhang, Ceng Zhang, Saeed Sadeghi, Richard S. Finn, Sammy Saab, Ronald W. Busuttil, Yazhen Zhu, Hsian-Rong Tseng, Sungyong You, Ju Dong Yang, Vatche G. Agopian. Circulating tumor cell-based mRNA scoring system for prognostication of hepatocellular carcinoma - Translating HCC tissue-based mRNA profiling into a non-invasive setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 764.