Abstract 7503: Detection of genomic alterations in lenvatinib-resistant liver cancer cell lines

Abstract Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, is the sixth most prevalent tumor worldwide and the fourth leading cause of cancer-related deaths. Lenvatinib, a multi-targeted tyrosine kinase inhibitor (TKI), is a first-line therapy for HCC patients who are ineligible for immunotherapy. However, like other targeted therapies, its efficacy is often compromised by the development of resistance. Understanding the molecular alterations driving this resistance is critical to improving therapeutic outcomes in HCC. In this study, lenvatinib-resistant human HCC cell lines were established by exposing parental sensitive cells to increasing concentrations of lenvatinib. Resistant Hep3B and Huh7 cell lines were successfully developed, exhibiting higher lenvatinib-specific IC50 values compared to their sensitive counterparts. To investigate the mechanisms underlying drug resistance, whole-genome sequencing (WGS, average depth: 30X) was performed, identifying resistance-specific genomic alterations, including copy number variations (CNVs), mutations, and structural variations (SVs). Emerging evidence suggests that chromosomal instability (CIN) plays a critical role in resistance evolution through structural rearrangements and focal amplifications. To reconstruct these amplified regions, we utilized AmpliconArchitect, followed by classification into chromosomal amplification (ChrAmp) and extrachromosomal DNA (ecDNA) using AmpliconClassifier. The number of focal amplifications increased from 4 to 7 in resistant Hep3B cells and from 14 to 18 in resistant Huh7 cells. Notably, newly identified oncogenes were detected within these amplicons, including ZIC2 in Hep3B and EGFR in Huh7. Despite the emergence of new amplicon profiles in resistant cells, most retained their original classifications as ecDNAs or ChrAmps, suggesting that clones carrying these amplicons exhibit an intrinsic resistance phenotype. Ongoing studies involving single-clone isolation and further genomic characterization aim to refine and expand these findings. In conclusion, we successfully established lenvatinib-resistant HCC cell lines and characterized their resistance-specific genomic alterations. Our results highlight the role of CIN in driving resistance under the selective pressure of targeted therapies, offering potential insights for improving therapeutic strategies in HCC. Citation Format: JungHyun Kim, Ji Young Kim, Gamin Han, BoYoon Kim, Hoon Kim, Yeup Yoon, Wonseok Kang. Detection of genomic alterations in lenvatinib-resistant liver cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7503.