Fig. 5: Spatial analysis of IFN-rich domains and distinct T cell lineages.
From: Highly multiplexed 3D profiling of cell states and immune niches in human tumors
a, Three selected channels of 54-plex 3D CyCIF image of the MIS in dataset 2 (LSP13625). A maximum intensity projection of 116 planes is shown. IFN-rich domains are denoted by dashed circles. DEJ is denoted by a white dashed line. Scale bar, 100 µm. b, A magnified view of the inset from a showing same cell nuclear localization of IRF1, expression of MX1 and MHC-1 upregulation. DEJ is denoted by a white dashed line. The white arrowheads denote the invasion of melanocytic cells into the dermis. Scale bar, 25 µm. c, The enlarged inset from a, showing diversity of immune cells crossing the DEJ. DEJ is denoted by the white dashed lines. d,e, A maximum intensity projection of an activated TPEX cell, showing intracellular organelles such as GZMB (d) and membranous proteins such as LAG3 and PD1 (e). f, A 3D rendering of a TMEM cell interacting with a TPEX cell, which is in turn interacting with a cluster of metastatic melanoma tumor cells. Dendritic cells surround the neighborhood. g–j, The TMEM and TPEX cells shown in f, as a maximum projection (CD103, PD1, TCF1, TIM3 (g) and LAG3, CD8, PCNA (h) and 3D rendering (i and j). k, A hierarchical tree diagram showing proportions of CD8+ T sublineages the metastatic melanoma specimen. TMEM (magenta), TPEX (orange) and TEFF (blue) subtypes overlap, giving rise to four hybrid populations (TPOP1-4) as denoted by vertical labels (see ‘Progenitor and TEFF subsets’ for details). The red arrows denote additional cell subsets that are not shown on this tree. l, The percent of cells positive for GZMB (red) or MX1 (yellow) by population. See Supplementary Fig. 13 for a detailed diagram of which markers were used to define each cell type.
