Fig. 3: Quantification of intra-cell versus inter-cell isoform heterogeneity in colorectal metastasis to the liver.

A The UMAP of the colorectal cancer metastasis to the liver (CRCLM) single cell data, each point is a cell colored by its cell type definition. B The paired VISIUM sequencing for the same CRCLM sample. The left plot shows the histology, indicating the tumor region. The right plot shows the dominant cell type in each spot. C The relationship between \(\bar{\psi }\) and \(\phi\), \(\bar{\psi }\) means the mean of percent-spliced-in for an exon across the cell population, \(\phi\) means the inter-cell heterogeneity of this exon. The histograms of \(\psi\) are colored by their \(\bar{\psi }\). The dots above each histogram show the alternative splicing across the cell population. The dot filled in red means the target exon is preserved in the isoforms in this cell, while the dot filled in white means the target exon is spliced out. The circle filled in red gradient means the cell expresses both isoforms. D ϕ vs. \(\bar{\psi }\) distribution for alternative spliced exons in CRCLM single cell data, the color indicates the confidence interval of ϕ estimation. E The \(\psi\) distribution for exon 6 of MYL6, which has a very high ϕ, indicating high intercell heterogeneity. In this histogram, x-axis shows the exon \(\psi\) and y-axis shows the cell frequency whose \(\psi\) value falls in this bin. As \(\psi\) estimation is influenced by the gene expression, the average gene expression for is bin is shown in color gradient. F The left plot shows the ψ distribution for exon 6 of MYL6 across cells, epithelial show the highest inclusion-level of this exon. The expression of two dominant isoforms across different cells are shown in the right heatmap, epithelial has higher expression of MYL6-218 compared to other cell types. G The sashimi plot shows the comparison of bulk expression of MYL6-207 and MYL6-218 between epithelial cells and other immune cells. H The spatial view of the expression for MYL6-218 (top) and MYL6-207 (bottom). The regions for myeloid cells are marked by black circles. Source data are provided in https://doi.org/10.5281/zenodo.15320816.