Extended Data Fig. 4: CRISPR screen of foamy macrophage oxLDL uptake and scavenger receptor expression.
From: Trem2 promotes foamy macrophage lipid uptake and survival in atherosclerosis
a) Time course analysis of DiI-oxLDL uptake in WT BV2 cells differentiated in media with 20 µg/mL of soluble cholesterol overnight prior to addition of DiI-oxLDL (n = 5 biological replicates/group). Data are mean ± S.E.M. b) CRISPR guide enrichment by rank-order was plotted against P-value for DiI-oxLDL-low compared against DiI-oxLDL-high to identify top enriched guides. Trem2 in red. P-values calculated using the negative-binomial model from MAGeCK package and adjusted using Benjamini-Hochberg procedure. c) Two sided P-value vs count and p value vs false discovery rate (FDR) for DiI-oxLDL-low compared against DiI-oxLDL-high to identify top enriched guides. p-values and FDR calculated using the negative-binomial model from MAGeCK package and adjusted using Benjamini-Hochberg procedure. d) Top 15 ‘importance index’ genes associated with foamy cell commitment by Trade-seq analysis (Fig. 1), were compared for gene rank and enrichment in CRISPR screen. Trem2 highlighted in gray. P-values calculated using the negative-binomial model from MAGeCK package and adjusted using Benjamini-Hochberg procedure. e) CD36 expression (left) and percent CD36 high (right) of foamy peritoneal macrophages cultured with soluble cholesterol overnight from WT (blue) and Trem2-/- mice (red). Gated on F4/80+ CD11b+ live cells (n = 5 biological replicates/group). Data are mean ± S.E.M. Student’s t-test, P = ** < 0.01. f) SR-AI expression (left), MFI (middle) and percent SR-AI positive (right) of foamy peritoneal macrophages cultured with soluble cholesterol overnight from WT (blue) and Trem2-/- mice (red). Gated on F4/80+ CD11b+ live cells (n = 5 biological replicates/group). Data are mean ± S.E.M. Student’s t-test
