Both tumor and normal liver tissues were macro-dissected, and total RNA was extracted using the All Prep DNA/RNA FFPE Kit (Cat #80234, Qiagen, Germantown, MD) following the manufacturer's protocol. The integrity and quantity of isolated RNA were evaluated using the Tape Station with High Sensitivity RNA Screen Tape (Cat #5067–5579, Agilent Technologies, Santa Clara, CA) and Qubit RNA assay kit (Cat #Q32855, Invitrogen, Thermo Fisher Scientific, Waltham, MA). For RNA library preparation, we utilized the SureSelectXT Low Input library preparation and target enrichment kit (Cat #5190–9686, Agilent Technologies, Santa Clara, CA). Libraries were pooled in 12-plex format and sequenced to a read depth of 30 million reads per sample using single-end reads on the NextSeq 500/550 platform with the High Output reagent cartridge v2 (Cat #, 15057934, Illumina, San Diego, CA).