Extended Data Fig. 10: Transcriptional profile of stem-immunity hubs, non-stem-immunity hubs, and TLS using GeoMx. | Nature Immunology

Extended Data Fig. 10: Transcriptional profile of stem-immunity hubs, non-stem-immunity hubs, and TLS using GeoMx.

From: Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy

Extended Data Fig. 10

(a, b) Comparison of (A) stem-immunity hub and non-stem-immunity hub and (B) non-stem-immunity hub and TLS gene expression using GeoMx CTA assay. Volcano plots depict pooled ROIs across all 5 samples. Each dot represents one gene. Dot coloring is as follows: blue - ISGs, green - myeloid genes, purple - T cell genes, and orange - B cell genes. (c) Scatter plot of expression for 177 genes included in both GeoMx and MERFISH panels for manually annotated stem-immunity hubs (GeoMx) and tile cluster-defined stem-immunity hubs (t7, MERFISH) (pearson correlation r = 0.78, p < 1E-35). Axes indicate log2 fold-change of gene expression in stem-immunity versus non-stem-immunity hub. Each dot denotes one gene. Red dots denote the top 10 over-expressed genes in stem-immunity (versus non-stem-immunity hub) in the GeoMx dataset.

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