Skip to main content
. 2023 Jun 23;12:e86125. doi: 10.7554/eLife.86125

Figure 2. Overview of gene expression data from spatially-defined stromal and immune regions within the PDAC tumor microenvironment using NanoString GeoMx DSP.

(A) Expression profile of all endogenous probes across regions of interest (ROI) with hierarchical clustering of ROIs. (B) UMAP embedding from normalized count data showing all ROIs overlaid with ROI-specific annotations of Region (Immune/Stroma/Tumor type) and Survival (1 yr/3 yr). (C) Mean normalized count of cell type marker genes within regions. Lines indicate regions from the same patient; dashed line represents mean background threshold from negative probes; Mean +/-SE of mean shown in red. (D) Differential expression analysis to identift genes expressed differentially between Immune and Stroma ROIs. Colored points indicate differentially expressed genes (DEG) (BH adjusted p<0.05 and absolute log2FC >0.25). (E) Immune and Stroma expression signatures from DEGs identified in D.

Figure 2.

Figure 2—figure supplement 1. Raw count expression profiles.

Figure 2—figure supplement 1.

(A) Heatmap of raw expression profile for the complete probeset (colour scale = raw count). (B) Per patient (scan) expression distributions for PanCK+ (tumor) and PanCK- (non-tumor) regions of interest. (C) Per patient (scan) expression profiles (mean +/-SE) for Endogenous, Housekeeping and Negative control probesets.
Figure 2—figure supplement 2. Housekeeping gene correlations and data normalisation.

Figure 2—figure supplement 2.

(A) Pairwise correlation scatter plots for 6 housekeeping control probes. Raw housekeeping gene counts from all regions of interest (ROIs) were correlated against each other. Plots display the scatter, distribution histogram and Pearson correlation coefficient and significance (***p<0.001). (B) Relative log expression plots of raw count data and post normalization with the top two most-correlated housekeeping genes (H3F3A and UBB) to remove unwanted variation (RUV method).
Figure 2—figure supplement 3. Correlation matrix of endogenous probes.

Figure 2—figure supplement 3.

Pairwise correlations of normalized gene count data represented as a matrix of Pearson correlation coefficients.
Figure 2—figure supplement 4. Individual gene expression profiles on UMAP embeddings of all regions of interest (ROIs).

Figure 2—figure supplement 4.

UMAP embedding generated from normalized count data of all probes in all REIs overlaid with ROI-specific normalized gene count.
Figure 2—figure supplement 5. High level cell type contexture of PDAC tumor microenvironment.

Figure 2—figure supplement 5.

(A) (left), UMAP embedding of transcriptional data for 17,958 cells in the tumor microenvironment of 3 x PDAC patient tissue samples overlaid with high level cell type identified from unsupervised clustering. A (right), UMAP embedding overlaid with source sample identifier. (B) UMAP embedding overlaid with the expression profile of canonical high level cell type marker genes. (C) Average scRNA expression profile of spatial profiling defined Immune and Stroma ROI type-associated genes within high level cell types defined by scRNA-seq (n=3 PDAC samples).