Fig 2: Experimental validation of RF-related tumour macrophage infiltration. (A) Scheme of the experimental workflow. (B) t-Distributed stochastic neighbour embedding (tSNE) plot shows clustering of each patient’s cells based on gene expression. Point coordinates are based on tSNE dimensionality reduction of the top principal components calculated from the 5000 most informative genes. Cell colour specifies assignment of cells to these clusters inferred using shared nearest neighbour clustering. Pie charts demonstrate the distribution of the identified cell types across samples in each patient and histograms show the macrophage cell abundance between high-risk and low-risk patients. (C) Immunohistochemical staining displays the RF-related macrophage markers MS4A4A, STAB1 and COLEC12. The scatter diagram shows the expression level of these markers in high-risk and low-risk samples. Kaplan–Meier survival analysis was performed between the samples with high and low expression of macrophage markers.

Fig 3: Expression of MS4A genes during in vitro monocyte to Mϕ differentiation. mRNA expression of MS4A4A (A), MS4A6A (B), MS4A7 (C), and MS4A14 (D) genes during in vitro M‐CSF‐dependent monocyte to Mϕ differentiation. (A‐D) Data are presented as relative expression to GAPDH. Results are shown as median ± IQR, and each symbol represents a different biological replicate. N = 4–6 (per group). Statistical analysis was performed by Kruskal‐Wallis test with a Dunn's multiple comparison test; P ≤ 0.05 was considered significantxs

Fig 4: Expression of MS4A genes in lung and BALF of COVID‐19 patients. (A) U‐map single cell RNA‐seq analysis BALF of COVID‐19 patients showing different cell population (multicolor panel) and MS4A3, MS4A4A, MS4A6A or MS4A7 expression in those populations (green‐to‐blue panels). The data were retrieved from the COVID‐19 Cell Atlas with the ID “Bronchoalveolar lavage fluid VIB‐UGent”, Ballestar E. et al. (unpublished) (2021). 53 (B) Expression of MS4A4A and CD68 in lung tissue of deceased patients with SARS‐CoV‐2 positive pneumonia. 5μm serial slices of paraffin embedded lung samples were stained with rabbit anti‐human MS4A4A or mouse anti‐human CD68 (brown) and counterstained with hematoxylin (blue)

Fig 5: Expression of MS4A proteins in human tissues. Expression of MS4A3, MS4A4A, MS4A4E, MS4A7 (A), and MS4A14 (B) proteins in human tissue. Three micrometer slices of paraffin embedded lung and colon (A) or testis (B) tissue samples were stained with rabbit anti‐human MS4A3, MS4A4A, MS4A4E, MS4A7, and MS4A14 (brown) and counterstained with hematoxylin (blue). Figure (20×) and insert (40×) represent the expression in the normal/healthy portion of the sample