Extended Data Fig. 9: Additional scRNA-seq analysis of primary HNSCC samples and scRNA-seq analysis using public domain data from Puram et al. (2017)34. | Nature Methods

Extended Data Fig. 9: Additional scRNA-seq analysis of primary HNSCC samples and scRNA-seq analysis using public domain data from Puram et al. (2017)34.

From: Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA

Extended Data Fig. 9: Additional scRNA-seq analysis of primary HNSCC samples and scRNA-seq analysis using public domain data from Puram et al. (2017)34.The alternative text for this image may have been generated using AI.

(a) UMAP plot of identified cell clusters with node status on the study HNSCC cohort. (b)-(c) UMAP plots highlighting expression of FOXP3, IL2RA, CXCR3, CD4 and CD8A. (d) CXCR3 expression in different T cell clusters showing that CXCR3 is differentially expressed in N0 (n = 2) versus N + (n = 2) samples only in the Treg cells. (e) Violin plot of STAT1 expression in the Treg cluster between N + (n = 2) and N0 (n = 2) samples. STAT1 is a CXCR3 inducer. (f) Violin plot of CXCL9 and CXCL11 in the malignant cell cluster between N + (n = 2) and N0 (n = 2) samples. CXCL9 and CXCL11 are both ligands of CXCR3, but they are not differentially expressed in our data. (g) Heatmap shows expressions of CD274 (PD-L1), MUC1, EMT markers (CDH1 and VIM) and stemness markers (CD44 and CD24). (h) UMAP of identified cell clusters using the Puram et al. dataset. (i) UMAP of identified cell type clusters with node status color-coded. (j) UMAP plots of CD4, CD8A, and FOXP3. (k) UMAP plot of CXCR3. (l) Violin plots of CXCR3 in the T cell clusters between N + (n = 12) and N0 (n = 6) samples. (m) Violin plot of CXCL10 in malignant cell cluster 0 between N + (n = 12) and N0 (n = 6) samples. Differentially expressed genes were identified using SAMR and false discovery rate was used to adjust p-values. Center line of box plot defines data median, top value indicates largest value within 1.5 times interquartile range above 75th percentile, bottom value indicates smallest value within 1.5 times interquartile range below 25th percentile, and upper and lower bounds of the box plot indicate 75th and 25th percentile respectively. *: adjusted p-value < 0.05, **: adjusted p-value < 0.01, ***: adjusted p-value < 0.005, ****: adjusted p-value < 0.001.

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