Multi-omics limitations in patient-derived cancer organoids: molecular origins and strategies for mitigation

Abstract

Patient-derived organoids (PDOs) are widely used platforms for cancer modeling and precision oncology because they preserve patient-specific genetic backgrounds, recapitulate aspects of native tissue architecture, and allow long-term expansion, repeated functional interrogation, and drug screening. Accordingly, multi-omics profiling of PDOs—encompassing genomics, transcriptomics, epigenomics, and proteomics—has been increasingly used to examine tumor heterogeneity, clonal evolution, molecular subtypes, and drug-resistance mechanisms at high resolution. However, accumulating evidence indicates that PDOs do not fully reproduce the molecular state of their parental tumors and that the extent and nature of this divergence vary systematically across omics layers. At the genomic level, sampling bias, clonal selection, ongoing chromosomal instability, and mismatch repair–dependent mutational dynamics can reshape subclonal architecture during organoid establishment and passaging. At the transcriptomic level, loss of the tumor microenvironment, molecular subtype drift, and culture-adaptive changes in unfolded protein response and metabolic programs can generate expression states that differ from those of primary tumors. At the epigenomic level, DNA methylation drift—sometimes resembling aging-associated trajectories—may accumulate during long-term culture. At the proteomic level, transcriptome–proteome discordance, Matrigel-derived contamination, and incomplete recapitulation of the tumor-intrinsic extracellular matrix and secretome constrain interpretation. This review systematically classifies these layer-specific limitations, examines their molecular origins, and summarizes mitigation strategies, including multi-region sampling, early-passage analysis, paired profiling with matched tumors, microenvironmental reconstitution, and integrative multi-omics frameworks. The value of PDO-based omics lies not in perfect molecular fidelity, but in defining precisely which molecular features are preserved and which are remodeled.