Chemical induction enhances patient-derived organoid fidelity to primary colorectal cancer at the single-cell level: A re-analysis of public scRNA-seq dataset GSE261012.

BACKGROUND: Patient-derived organoids (PDOs) are widely used preclinical models for colorectal cancer (CRC). However, conventional PDO cultures frequently lose tumor microenvironment (TME) components and undergo culture-induced transcriptional drift. A chemically defined induction system (CiPDO) has been proposed to preserve fetal-like plasticity states, yet a direct single-cell comparison of CiPDO versus conventional PDO against the matched primary tumor is lacking. OBJECTIVE: To evaluate and compare the single-cell transcriptional fidelity of chemically induced PDO (CiPDO) and conventional PDO (current_PDO) relative to the matched primary colorectal tumor, using a publicly available scRNA-seq dataset. METHODS: We re-analyzed the public scRNA-seq dataset GSE261012, which profiled cells from the primary tumor, conventional PDO (current_PDO), and chemically induced PDO (CiPDO) of the same CRC patient. Using Scanpy, we performed quality control, clustering, cell type annotation, and module scoring for oncofetal-like state (OnFS), proliferation, stress/hypoxia, epithelial-mesenchymal transition (EMT), and differentiation signatures. All possible pairwise comparisons among the three conditions were performed using two-sided Mann-Whitney U tests. For each module score, we provided biological interpretation of the score magnitude, reference ranges from established CRC single-cell atlases, and contextualization of the observed values. RESULTS: After quality control, 16,249 cells were retained across 19 clusters. Both PDOs completely lost TME components (fibroblasts, myeloid, T cells) compared with the primary tumor. At the epithelial-cell level, CiPDO showed significantly higher OnFS scores than current_PDO (0.189 vs. 0.102, p < 0.001) and both PDOs exhibited significantly higher OnFS than the primary tumor (-0.232; both p < 0.001). Proliferation scores were highest in the primary tumor (1.461), intermediate in current_PDO (0.983), and lowest in CiPDO (-0.314); all pairwise differences were significant (p < 0.001) except primary tumor vs. current_PDO (p = 0.082). Stress/hypoxia scores were significantly elevated in current_PDO (0.286) compared with both CiPDO (0.052, p < 0.001) and the primary tumor (0.195, p = 0.041). Differentiation scores did not differ significantly between the two PDO conditions (p = 0.171), whereas both PDOs showed significantly higher differentiation than the primary tumor (both p < 0.001). EMT scores showed a small but statistically significant difference between CiPDO (-0.078) and current_PDO (-0.098, p < 0.001), and both were significantly higher than the primary tumor (-0.128; both p < 0.001). CONCLUSION: Within the constraints of a single-patient design, CiPDO better preserves the oncofetal-like plasticity state of primary CRC epithelial cells while exhibiting fewer culture-induced proliferation and stress signatures than conventional PDO. Differentiation states were comparable between the two PDO conditions. These findings support the use of chemically defined induction to improve PDO fidelity for studying tumor cell plasticity, although validation in larger cohorts is required.

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Authors

Libo F; Dong X; Yu L

Published

Jan 1, 2026

Journal or venue

Biochemical and biophysical research communications

DOI

10.1016/j.bbrc.2026.154396

Paper type

journal article

Source

Pubmed