Journal: Communications biology

Article Title: Single-cell profiling of the microenvironment in human bone metastatic renal cell carcinoma.

doi: 10.1038/s42003-024-05772-y

Figure Lengend Snippet: Fig. 6 The differential trajectory of myeloid cell subtypes in the BMRCC. a Developmental trajectory of MDSC and macrophage subtypes in the BMRCC. Colors of cell indicate cell type marked by legend. b The expression patterns of genes associated with the pseudotime and their functional enrichment. Colors on heatmap indicate the genes expression. Color from red to blue indicates a high to low expression. c. The expression levels of phagocytosis signatures among the macrophage subtypes in BMRCC. Colors on the columns indicate cell type marked by x-axis. P values were calculated by Kruskal −Wallis test, n = 5172 biologically independent cells. d Comparison of the M1- and M2-associated signature gene expression levels in the Macro-NRP2 cells in BMRCC. Blue columns indicate M1 type, yellow columns indicate M2 type. P values were calculated by Student’s t test, n = 887 biologically independent cells. Effect size of Cohen’s d: 1.826. e The expression levels of M2-associated signature genes in Macro-NRP2 among the primary ccRCC of early and advanced stages and BMRCC. Blue columns indicate primary ccRCC early group, yellow columns indicate primary ccRCC advanced group. The gray columns indicate BMRCC group. P values were calculated by Student’s t test, n = 1833 biologically independent cells. Effect size of Cohen’s d: primary ccRCC early group vs BMRCC: 1.059; primary ccRCC advanced group vs BMRCC: 0.811. f mIHC showing the existence of Macro-NRP2 in BMRCC. The green color indicates the expression of SPP1 protein. The red color indicates the expression of NRP2 protein. The purple color indicates the expression of CD68 protein. Box-and-whisker plots (c–e): centre line indicates median, box represents first and third quantiles, and whiskers indicate maximum and minimum values.

Article Snippet: Formalin-fixed, paraffinembedded (FFPE) tissues containing primary and bone metastatic tumors of RCC were sliced into 4 μm sections and stained with antibodies against FAP (abcam, ab218164, Rabbit pAb, 1:1000), Vimentin (CST, 5741, Rabbit mAb, 1:1000), CD8A (abclonal, A0663, Rabbit mAb, 1:1000), PD-1 (abclonal, A20217, Mouse mAb, 1:1000), GZMB (abclonal, A22993, Rabbit mAb, 1:1000), CD68 (abclonal, A23205, Rabbit mAb, 1:1000), NRP2 (proteintech, 11268-1-AP, Rabbit pAb, 1:1000), SPP1 (proteintech, 22952-1-AP, Rabbit pAb, 1:1000), CD47 (SCBT, sc12730, Mouse mAb, 1:500), and SIRPA (abcam, ab260039, Rabbit mAb, 1:1000) according to the standard protocols.

Techniques: Expressing, Functional Assay, Comparison, Gene Expression, Whisker Assay