Extended Data Fig. 9: Single cell transcriptomics of case F44P1 and integration with other single-nuclei FA SCC samples.
From: Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer
a Feature plots superimposed on a UMAP embedding displaying cell type identity markers corresponding to the annotated clusters in Fig. 4g. Macrophage (CD163), CD4+ T-cells (CD4), CD8+ T cells (CD8A), KRT14/5+ tumor keratinocytes (KRT14), neutrophils (HCAR2), fibroblasts (COL11A1), mast cells (TPSAB1), Langerhans dendritic cells (CD207), p-EMT tumor keratinocytes (LAMA3), myofibroblasts (ACTA2), differentiated tumor keratinocytes (SPRR2E), endothelial cells (VWF). See methods for additional markers used for identification. b ASCAT plot of WGS sample F44P1 (top), inferred single-cell copy-number analysis displaying distinct amplifications in tumor keratinocyte, p-EMT tumor keratinocyte, and differentiated tumor keratinocyte clusters (bottom) c Feature plot displaying the scTSK sensor score for case F44P1. d Feature plots displaying a selection of scTSK markers. e Feature plot displaying p-EMT sensor score for case F44P1. f Feature plots displaying a selection of p-EMT markers. g Fold-enrichment in gene expression between p-EMT vs non-EMT tumor keratinocytes in F44P1 (DESeq2 log2(x) > 0.2, Wald test with FDR-adjusted p-value < 0.05) shown by GO term. GO enrichment Fisher’s exact test FDR-adjusted p-value displayed. h UMAP embedding displays the integrated clustering of F44P1 (single-cell), F46P1 (single-nuclei), and F38P1 (single-nuclei) samples after quality control (k = 1,986 cells). Cell type identities are indicated in the legend. i scTSK and p-EMT sensor scores of integrated samples, split by constituent tumor sample. Also see Supplementary Fig. 1 for examples of cellular markers used in h and i.
