Fig. 2

A progressive epithelial differentiation, but no strong uniform direction of development in pEMT clusters. A UMAP of 1906 OSCC cells annotated based on SNN clustering, defining 4 pEMT (pEMT-1 to 4), 4 epithelial differentiated (epi-1 to 4) and one mixed (mix) cluster; clusters are numbered by size. B Heatmap for scaled, log-normalized gene expression in EMP-associated tumor cell phenotypes (columns) split by EMP cluster and their top 5 DEGs (rows) against all other EMP-related tumor cell phenotypes. DEGs are sorted from highest to lowest log2 foldchange. Row sections are ordered like column sections. C Projection of RNA velocity on the UMAP depicted in A. Arrows indicate the extrapolated direction of development; arrow length indicates strength of future development. D First two principal components of OSCC cells with the three EMP-related principal curves that are derived from trajectory inference. Graph on top visualizes the relationship between EMP clusters described by the three principal curves forming a branching trajectory. E Log-normalized expression (y-axis) of MMP1, VIM, SPRR1B and KLK7 across pseudotime values (x-axis) of curve 2, color-coded by clusters. Red lines indicate smoothed expression values over the trajectory generated with a general additive model; 95% confidence intervals are shaded gray. F Inferred CNVs across EMP-related tumor cells (rows) for all chromosomes (columns). Red indicates copy number gains, white diploid copy number and blue copy number loss. Columns show genes categorized in chromosomes and ordered by genome position; hence the size of the chromosome reflects the number of detected genes and not its nucleotide length. Mitochondrial genes were excluded