Fig. 5
From: Long-term maintenance of patient-specific characteristics in tumoroids from six cancer indications
OncoPro medium-derived tumoroid transcriptomes are stable during long-term culture. (a) Principal component analysis (PCA) of global gene expression patterns in human colorectal (HuCo) and lung (HuLu) tumoroid cultures over multiple passages (P). (b) Differential gene expression (DEG) analysis of early- versus late-passage tumoroids, with DEGs called at fold change > 2 and false discovery rate (FDR) < 0.05, for HuCo and HuLu samples. Pathway analysis of DEGs revealed few significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (FDR < 0.05) in late-passage colorectal tumoroids and early-passage lung tumoroids; the top 10 KEGG pathways for colorectal and lung tumoroids are shown. No KEGG pathways were enriched in early-passage colorectal tumoroids or late-passage lung tumoroids. Dotted line indicates FDR = 0.05. (c) Consensus molecular subtypes from gene expression analysis of colorectal patient-derived tumoroids through multiple passages. (d) Uniform Manifold Approximation and Projection (UMAP) for dimension reduction plot of single-cell RNA sequencing data from 4,905 total cells for HuCo021320 (early, P10; and late, P27) and HuCo3209 (early, P10) tumoroid cultures. HuCo3209 was used as a control donor for comparison. (e) Single cell copy number variation (CNV) plots for HuCo021320 (n = 4,973 genes, by column) of early (P10) and late (P27) passage tumoroid cultures. Each row represents one cell. InferCNV was used to estimate CNV in epithelial cells, using immune cells present in dissociated tumor tissue (P0) as reference.
