Figure 4

Macrophage chromatin accessibility also reverts to a baseline state when polarizing cytokines are removed. (A) Schematic of experimental design, where each point represents a collected sample, and each colored trajectory represents a different treatment condition. Murine bone marrow-derived macrophages were treated with IFN-γ + LPS to induce polarization to M1. After 24 h, cells were washed to remove cytokines and then cultured in base media with no polarizing cytokines for an additional 72 h (n = 3). (B) Bar plot depicts Jensen–Shannon distance (JSD) between the ATAC accessibility profiles of polarized and depolarized macrophages compared to the 0 h M0 control. As a baseline for expected global expression differences between samples, the teal line shows the average inter-replicate JSD between the three replicates for the 0 h M0 control sample. JSD values for 24 M1 and 72 h M1 → M0 conditions were computed as the average of JSDs for all unique pairs between the three replicates of each treatment condition and the three replicates of the 0 h M0 control. (C) Density plots of log2 fold-change (absolute value) of chromatin accessibility for M1-polarized macrophages and M1 → M0 depolarized macrophages compared to the baseline M0 condition. Median magnitude of log2 fold-change in chromatin accessibility is smaller for the M1 → M0 depolarized macrophages compared to the M1-polarized macrophages. (D) Scatterplot comparing log2 fold-change of chromatin accessibility for M1-polarized macrophages versus M0 (x-axis) and M1-polarized macrophages versus M1 → M0 depolarized macrophages (y-axis). The red line (y = x) indicates the expected correlation in the case where M1 → M0 depolarized macrophages are identical to M0 macrophages.