Extended Data Fig. 8: Gene expression changes along Palantir pseudotime for squamous and neuroendocrine trajectories.

a, UMAP of 3351 cells from KG146 primary tumour, synchronous liver metastasis, and metachronous lung metastasis. Cell are coloured by maximum module score, or grey if no module score exceeds its 25th percentile (top-left); by Palantir pseudotime (top-middle); by Palantir branch probability for the squamous-annotated (top-right) and neuroendocrine-annotated (bottom-left) branches; or by the fetal signature (bottom-left). b, Pearson correlations of Palantir⁴² branch probabilities with the expression of genes associated with squamous (top) and neuroendocrine (bottom) transdifferentiation, across tumours from patients KG146, KG182 and KG150. c, Gene expression trends along Palantir pseudotime for selected signalling pathways during trans-differentiation of KG146 tumour cells toward squamous or neuroendocrine-like terminal states. Trends are computed using generalized additive models (GAMs) in Palantir. Solid lines represent mean expression, shaded regions represent 1 s.d.