Journal: Cell reports

Article Title: Nanoparticle-based itaconate treatment recapitulates low-cholesterol/low-fat diet-induced atherosclerotic plaque resolution

doi: 10.1016/j.celrep.2024.114911

Figure Lengend Snippet: (A) Ctrl/ITA-LNP were injected into wild-type mice followed by neutrophil isolation from bone marrow. Neutrophils were cultured and stimulated by LPS or TNF-α in vitro . (B) Cytokines in supernatants from (A) as determined by Luminex ( n = 7). Filled circles indicate p < 0.001. (C) Principal component (PC) analysis after bulk RNA-seq of mRNA obtained from (A). (D) GO analysis of Ctrl/ITA-LNP treated neutrophils with and without LPS stimulation. (E) ChIP-seq heatmaps showing acetylation of H3K27 near the transcription start site (TSS). The data were obtained from whole bone marrow cells in separate experiments conducted as shown in (A) but without stimulation in vitro . (F) Immunoblot probing for H3K27ac and pan-acetylated lysine (Kac) in lysates of cultured BMDMs treated with Ctrl/ITA-LNP. (G) Profiles of H3K27ac ChIP-seq occupancy and ATAC-seq in loci of the indicated genes from flow-sorted ITA-LNP-targeted bone marrow cells. See text and for identity of these cells. (H) WikiPathways GO analysis of gene set enrichments for downregulated genes in ITA-LNP vs. Ctrl-LNP groups from ATAC-seq datasets. (I) RNA-seq counts of histone acetylation regulating genes differentially expressed in whole bone marrow cells in separate experiments conducted as shown in (A) but without stimulation. Data are presented as mean ± SD. The p values were obtained from ANOVA with Tukey post hoc test.

Article Snippet: The sheared chromatin was immunoprecipitated with 1 μg of anti-H3K27ac ChIP grade rabbit polyclonal antibody (Millipore Sigma) with rabbit IgG used as a negative control.

Techniques: Injection, Isolation, Cell Culture, In Vitro, Luminex, RNA Sequencing, ChIP-sequencing, Western Blot