Systematic functional drug testing in patient-derived models reveals ex vivo sensitivities associated with clinical outcome in rare solid tumors

Abstract Rare cancers are individually uncommon but collectively represent a substantial share of cancer burden, with limited systemic treatment options for many entities. Molecular profiling identifies targetable alterations, but actionable findings are limited and responses can vary despite a matched target. This motivates complementary approaches that directly assess tumor drug response. Here, we establish a biopsy-compatible ex vivo drug sensitivity testing platform optimized for low input and reproducibility. Patient-derived material was tested either directly or following ex vivo expansion. Functional profiling was performed within clinically relevant timelines across models from 126 patients with rare advanced solid tumors. Drug responses were consistent between model types. In most samples, we identified at least one potentially active compound, supporting feasibility at biopsy-scale. High in vitro sensitivity was associated with clinical benefit and progression-free survival. These findings support functional drug sensitivity testing as a complementary component in precision oncology for adults with rare cancers. Statement of Significance This study presents a biopsy-compatible drug sensitivity testing platform for phenotype-based therapy stratification in rare cancers. It identifies actionable ex vivo drug responses and shows associations with clinical outcome in patients treated with screened therapies. These findings support functional testing as a complementary additional layer of stratification for therapeutic prioritization. Competing Interest Statement C.R.B. and I.O. received research funding from PreComb Therapeutics. C.H. received research funding and honoraria for advisory board participation from Boehringer Ingelheim and honoraria for speaking engagements from Roche and Novartis. LM: wife is an employee of Pfizer Pharma GmbH. Footnotes ↵* shared first author Conflict of Interest C.R.B. and I.O. received research funding from PreComb Therapeutics. C.H. received research funding and honoraria for advisory board participation from Boehringer Ingelheim and honoraria for speaking engagements from Roche and Novartis. LM: wife is an employee of Pfizer Pharma GmbH. Data Availability All data generated during this study are available from the corresponding author upon reasonable request. Raw reads are available from EGA (EGAD00001015778: Transcriptome sequencing dataset of rare tumors from the MASTER precision oncology registry, EGAD00001015777: Whole-genome sequencing dataset of rare tumors from the MASTER precision oncology registry, EGAD00001015804: Whole-exome sequencing dataset of rare tumors from the MASTER precision oncology registry) under controlled access. Abbreviations - 3D - Three Dimensional - BztZCl - Benzethoniumchloride - Cmax - Maximum Drug Serum Concentration in vivo - CR - Complete Response - CRC - Colorectal Cancer - CT - Computed Tomography - DMSO - Dimethyl Sulfoxide - DSS - Drug Sensitivity Score - DST - Drug Sensitivity Testing - CI - Confidence Intervals - CUP - Cancer of Unkown Primary - CNV - Copy Number Variants - FDR - False Discovery Rate - GC - Gastric Cancer - GOF - Goodness of Fit - HNC - Head and Neck Carcinoma - IC50 - Half-maximal Inhibitory Concentration - Hdels - Homozygous Deletions - HRD - Homologous Recombination - Indels - Small Insertions or Deletions - LC - Lung Carcinoma - LOH - Loss of Heterozygosity - LST - Large-scale State Transitions - LT - Long-Term - MAD - Median Absolute Deviation - MR - Mixed Response - MSI - Microsatellite Instability - N₂ - Nitrogen Gas - NSCLC - Non-small Cell Lung Cancer - NET - Neuroendocrine Tumor - NSG - NOD scid gamma - OC - Ovarian Carcinoma - PR - Partial Response - PDAC - Pancreatic Ductal Adenocarcinoma - PCM - Patient-derived Culture Models - PDX - Patient-derived Xenograft - PFS1 - Progression-free Survival Time 1 - PFS2 - Progression-free Survival Time 2 - PFSr - Progression-free Survival Ratio - PI1 - Percentage Inhibition at 1st drug concentration - PI5 - Percentage Inhibition at 5th drug concentration - QC - Quality Control - r - Spearman’s Rank Correlation - RCC - Renal Cell Carcinoma - RNAseq - RNA sequencing - RT - Room Temperature - SARC - Sarcoma - SC - Sensitivity Criteria - sCNAs - Somatic Copy Number Alterations - SD - Stable Disease - SNV - Single Nucleotide Variant - Sph - Spheroid - ST - Short-Term - TCC - Tumor Cell Content - TMB - Tumor Mutational Burden - TSO500 - TruSight Oncology 500 - WCSS - Within-cluster Sum of Squares