Patient-derived organoids inform pharmacogenomic vulnerabilities in liver cancer

Abstract

Background & Aims

Patient-derived tumor organoids (PDTOs) are a reliable model for preclinical and translational studies. Despite positive retrospective correlations with patient response, challenges such as culture success, cost, standardization, and time constraints hinder their clinical utility in precision medicine. Here, we optimize PDTO establishment using growth factor-reduced media (GF-) to mitigate these challenges and (1) identify somatic variant indicators that can improve the therapeutic index of existing FDA-approved drugs against hepatocellular carcinoma (HCC), (2) elucidate synthetic lethal candidates against undruggable HCC driver mutations, and (3) assess the feasibility of PDTOs in personalized therapy.

Methods

We successfully established a panel of 23 PDTOs from patients with HCC undergoing curative hepatectomy using a protocol primarily based on growth factor-reduced medium. PDTOs were subjected to comprehensive analyses, including the identification of hallmark mutations, assessment of genomic heterogeneity, transcriptomic profiling, and histological characterization. A 100-drug repurposing screen was conducted on the PDTOs and organoids derived from adjacent non-tumoral and normal livers to explore tumor-specific drug responses. Pharmacogenomic analysis using elastic net was performed (cut-off p <0.05) and synthetic lethality links were subject to experimental validation. The clinical relevance of PDTOs in personalized therapy were investigated through two case studies.

Results

Our results reveal that GF-derived PDTOs mimic histology and genetic heterogeneity of HCC. Pharmacogenomic analysis showed that the majority of tested FDA-approved drugs were not associated with HCC driver mutations (<5%). In addition, non-canonical signaling from CTNNB1 mutations were associated with ceritinib sensitivity (p <0.0001) via polypharmacological targeting of RPS6KA3. The PDTO case study showed clear benefit to patient survival by aiding clinical management.

Conclusions

Our findings underscore the utility of PDTOs established from minimal GF media in many facets of precision oncology advancements.

Impact and implications

Patient-derived tumor organoids are a reliable model for preclinical and translational studies. Despite positive retrospective correlations with patient response data, challenges such as culture success, cost, standardization, and time constraints hinder their clinical utility in guiding precision medicine. This study underscores the utility of patient-derived organoids established from growth factor-reduced media in many facets of precision oncology, showing for the first time in hepatocellular carcinoma, clear benefit to patient survival in a proof-of-concept case study.