Comparative Analysis of Patient-Matched PDOs Revealed a Reduction in OLFM4-Associated Clusters in Metastatic Lesions in Colorectal Cancer

Metastasis is the major cause of cancer-related death, but whether metastatic lesions exhibit the same cellular composition as primary tumors has yet to be elucidated. To investigate the cellular heterogeneity of metastatic colorectal cancer (CRC), we established 72 patient-derived organoids (PDOs) from 21 patients. Combined bulk transcriptomic and single-cell RNA-sequencing analysis revealed decreased gene expression of markers for differentiated cells in PDOs derived from metastatic lesions. Paradoxically, expression of potential intestinal stem cell markers was also decreased. We identified OLFM4 as the gene most strongly correlating with a stem-like cell cluster, and found OLFM4+ cells to be capable of initiating organoid culture growth and differentiation capacity in primary PDOs. These cells were required for the efficient growth of primary PDOs but dispensable for metastatic PDOs. These observations demonstrate that metastatic lesions have a cellular composition distinct from that of primary tumors; patient-matched PDOs are a useful resource for analyzing metastatic CRC. •Seventy-two PDOs were established from 21 stage IV CRC patients•Forty-one DEGs were identified between primary and corresponding metastatic PODs•scRNA-seq analysis identified OLFM4 as a potential cancer stem cell marker•Different roles of OLFM4+ cells in primary and metastatic PDOs were demonstrated In this article, Yao and colleagues show the cellular heterogeneity of PDOs derived from stage IV CRC. Primary PDOs possess more variable cellular hierarchy than corresponding metastatic/recurrent PDOs. OLFM4 is identified to be the gene most correlated to the stem cell-like clusters, and OLFM4+ cells are indispensable for the growth of primary PDOs.