Extended Data Fig. 2: Squamous features in PASC organoids.
a, Gene set enrichment analysis of PASC organoids versus non-PASC organoids. The genes were ranked according to the fold change value in differential gene expression analysis, and the enrichment of GOBP gene sets was analysed. Top five gene sets with positive or negative enrichment based on the adjusted P value are shown. NES, normalized enrichment score. b, Micrographs of PASC organoid xenografts. Wnt+ organoid (PC3) is shown for comparison. The PC88 tumour is a orthotopic xenograft, and the others are subcutaneous tumours. The four PASC lines analysed stain positive for squamous cell markers p63 and KRT5/6. Scale bar, 100 μm. c, Hierarchical clustering of ICGC (left) and TCGA (right) samples using the genes differentially expressed between PASC and non-PASC organoids (fold change > 4 or < 0.25, adjusted P value < 0.05 in DESeq). The samples were annotated according to their molecular subtypes, and histology for ICGC tumours. ADEX; aberrantly differentiated exocrine endocrine, IPMN; intraductal papillary mucinous neoplasm. d, Positive correlations between LGR5 and GATA6 expressions in PC organoids, and in the ICGC and TCGA cohorts. PASC organoids and the Squamous subtype tumours show low expressions of LGR5 and GATA6. r, Pearson correlation coefficient. Box plots represent the median (centre line), upper and lower quartiles (box limits), and 1.5 × interquartile ranges (whiskers).
