Fig. 7: Validation of two interaction pairs between tumor and TAM using RNAscope assay. | Nature Communications

Fig. 7: Validation of two interaction pairs between tumor and TAM using RNAscope assay.

From: Multiregional single-cell dissection of tumor and immune cells reveals stable lock-and-key features in liver cancer

Fig. 7

a Illustration of ligand–receptor interaction pairs between tumor cell and TAM (generated using BioRender). b A representative image of RNAscope multiplex fluorescent in situ hybridization of four genes of an HCC sample from a total of 258 samples analyzed. (c) Correlation of RNAscope signal and bulk transcriptome gene expression in TIGER-LC cohort. Pearson’s correlation coefficient (two-sided) was calculated. Dashed line: p = −log10(0.05). d Evaluation of the colocalization of two spatially distributed genes. BC, Bhattacharyya coefficient: 1, a full colocalization; 0, no colocalization. FTs, filled tiles. e The distribution of BCs of LGALS9 and SLC1A5 (top) as well as SPP1 and PTGER4 (bottom) in HCC samples from the TIGER-LC cohort. Dashed line: mean value. f The distribution of the proportion of filled tiles of LGALS9 and SLC1A5 (top) as well as SPP1 and PTGER4 (bottom) in HCC samples from the TIGER-LC cohort. Ten-times of randomization was used to generate random spread of markers on tissue sections as a reference. Gray line, proportion determined based on the ratio of true signal and each random spread; gold line, mean derived from ten gray lines. Dashed line: mean value. Student’s t-test (two-sided) was applied. g Overall survival of HCC patients with low expression and high expression of LGALS9 and SLC1A5 as well as SPP1 and PTGER4 from the TIGER-LC cohort. Tumor samples with expression of the four marker genes in between were grouped into others. Log-rank test and a trend test among the groups were preformed. h t-SNE plot of TAMs from samples with or without the two pairs (i.e., LGALS9 and SLC1A5, SPP1 and PTGER4) in Fig. 5a. i The composition of each TAM cluster. j Differentially expressed genes of TAMs from the samples with or without the two pairs (i.e., LGALS9 and SLC1A5, SPP1 and PTGER4) in Fig. 5a. k Differentially expressed genes of malignant cells from the samples with or without the two pairs (i.e., LGALS9 and SLC1A5, SPP1 and PTGER4) in Fig. 5a. Wilcoxon test with multiple test adjustment was applied in (j) and (k).

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