Fig. 4: Biofilm shows coordinated transcriptional regulation.
A S. aureus biofilm was grown for 4 days in RPMI-based medium under static, aerobic conditions at 37 °C with daily medium replenishment. After 4 days, biofilm was directly co-cultured with 5×105 mouse bone marrow-derived macrophages (MΦs), granulocytic myeloid-derived suppressor cells (G-MDSCs), or neutrophils (PMNs) for 2 h, whereupon immune cells were lysed with water. Cells from biofilm control (no immune cells) and the co-cultures were fixed overnight before permeabilization under identical conditions. Cells from each respective sample were separated for the first round of barcoding, then combined for the second and third rounds. The combined samples were processed through sequencing. Schematic created in BioRender: Korshoj, L. (2024) BioRender.com/z90k781. B UMAP plot of the biofilm control (n = 4655 cells), with colors denoting transcriptional subpopulations identified with the Leiden algorithm. C UMAP plots of independently clustered biofilms co-cultured with immune cells (n = 4544 cells for MΦ co-culture, n = 4780 cells for G-MDSC co-culture, n = 6125 cells for PMN co-culture). Responses to each immune population are explored in more detail in Fig. 6. D Transcriptional regulatory categories for the biofilm control are overlaid on UMAP plots. Categories correspond to the schematic in Fig. 3A. Color represents normalized expression score per cell.
