Molecular Indicators of Hepatocellular Carcinoma Resistance to Y-90 Microspheres Revealed Through High Throughput Screening of Cell Lines and Transcriptomics

Sunday, March 30, 2025

3:27 PM – 3:36 PM CT

Location: Music City Center, 207 CD

Presenting Author(s)

CM

Christopher Malone, MD

Associate Professor
Mallinckrodt Institute of Radiology, Washington University, United States

Author/Co-author(s)

AZ

Alexander Zheleznyak, MS

Staff Scientist
Washington University St. Louis, United States
DD

Dhanusha Duraiyan, MS

Bioinformatics Research Assistant
Division of Oncology, Department of Medicine. Washington University School of Medicine, United States
SW

Shuang Wu, MS

Senior Statistical Data Analyst
Department of Surgery. Washington University School of Medicine, United States
EL

Esther Lu, PhD, MS

Professor
Department of Surgery. Washington University School of Medicine, United States
JW

Jason Weber, PhD

Professor
Division of Oncology, Department of Medicine. Washington University School of Medicine, United States
DT

Daniel Thorek, PhD

Associate Professor
Mallinckrodt Institute of Radiology. Washington University School of Medicine, United States
RF

Ryan Fields, MD

Professor
Department of Surgery. Washington University School of Medicine, United States
MC

Matthew Ciorba, MD

Professor
Division of Gastroenterology, Department of Medicine. Washington University School of Medicine, United States
VB

Valerie Blanc, PhD

Assistant Professor
Division of Gastroenterology, Department of Medicine. Washington University School of Medicine, United States
ND

Nicholas Davidson, MD

Professor
Division of Gastroenterology, Department of Medicine. Washington University School of Medicine, United States
JS

Jessica Silva-Fisher, PhD

Assistant Professor
Division of Oncology, Department of Medicine. Washington University School of Medicine, United States

Purpose:

To understand the transcriptomic signatures of response to Y-90 microsphere treatment in hepatocellular carcinoma (HCC).

Materials and Methods: In vitro viability screening of 10 human immortalized HCC cell lines spanning multiple subtypes (Hoshida S1: SNU-387, SNU-423, SNU-475, SNU-449, SNU-398, MHCC97-H. Hoshida S2: HepG2, Hep3B, PLC/PRF/5. Undefined: SK-Hep-1) was performed after 10 days of treatment with escalating Y-90 glass microsphere (Therasphere, Boston Scientific) activities (0-20 MBq/ml) using MTT assay. Normalized area-under-curve (nAUC) values were identified from each cell viability experiment (closer to 1.0 indicating resistance). RNA was isolated from all cell lines at baseline and from surviving fractions after high activity (20 MBq/ml) Y-90 microsphere treatment in SNU-398 and HepG2. Transcriptome sequencing was performed to determine differential gene expression using EdgeR. In addition, genes whose expression correlated with Y-90 sensitivity was performed with elastic net regression algorithm (EN).

Results: Marked heterogeneity of response was seen across cell lines, with SK-Hep-1 (nAUC = 0.81-1.13) and SNU-387 (nAUC = 0.65-0.91) demonstrating highest resistance and PLC/PRF/5 demonstrating highest sensitivity (nAUC 0.39-0.52, one-way ANOVA p=0.0002 for SK-Hep-1 vs PLC/PRF/5 and p=0.006 for SNU-387 vs PLC/PRF/5). Y-90 resistant cell lines were Hoshida S1 subtype and demonstrated mesenchymal, stem-like phenotypes. EN analysis across all cell lines identified upregulation with Y-90 microsphere resistance in 18 protein-coding genes and one small nucleolar RNA (EN scores > 0.7). These genes are associated with DNA replication (CAVIN1, EN=0.96, R=0.96), cell surface adhesion (ITGA3, EN=0.91, R=0.79), and G-protein signaling (ARHGAP23, EN=0.98, R=0.96). We identified 705 overlapping significant differentially regulated genes after Y-90 treatment comparing SNU-398 and HepG2, with both cell lines having 66 up-regulated, 111 down-regulated, and 628 contrasting gene regulation in each cell line (p < 0.0005).

Conclusion: High throughput screening of human HCC cell lines with treatment of Y-90 microspheres demonstrates variable response to treatment and revealed a unique treatment resistance gene signature. Significant gene expression changes after Y-90 microsphere treatment were seen amongst the different cell line subtypes, further supporting the role of HCC biological heterogeneity in treatment response. This contributes towards molecular-based personalized dosimetry and provides insight into potential adjuvant combinations.