Immunomodulatory Microparticles Epigenetically Modulate T Cells and Systemically Ameliorate Autoimmune Arthritis - PubMed (original) (raw)

ATRA differentially modulates chromatin accessibility at Th17 and Treg associated loci in Th17 polarizing conditions. a) Scatterplots of ATAC‐Seq counts per peak comparing cells exposed to Th17 polarizing conditions treated with 1 × 10−9

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ATRA (+ATRA, n = 3) or without ATRA (−ATRA, n = 3). Experimental timeline was the same as that depicted in Figure 1a. Red corresponds to DARs enriched in the +ATRA condition, blue corresponds to DARs enriched in the −ATRA condition, and gray corresponds to common regions that are accessible in both conditions, but not significantly different. b) Boxplots of ATAC‐Seq counts per peak from +ATRA and −ATRA conditions at common (gray) or DARs enriched in either the +ATRA (red) or the −ATRA group (blue) from the comparison in (a). Boxes indicate interquartile range with whiskers ± 1.5 times this range and outlier points. c) Normalized ATAC‐Seq coverage at the Foxp3, Rorc, Il17a, Il17f, Il1r1, Il6ra, and Tnf loci in average representations of the +ATRA and −ATRA conditions. d) Heatmap of select Th17 and Treg associated genes visualized in (c) for −ATRA and +ATRA conditions with dendrograms showing relatedness of samples (columns) and individual genes (rows). e) Heatmap of all DARs quantified by _z_‐score. DARs enriched in the +ATRA condition correspond to the red dots in (a), while DARs enriched in the −ATRA condition correspond to the blue dots in (a). f) Motif enrichment analysis for the grouped DARs in (e) quantified by enrichment of motif across clusters shown in (e) with enrichment quantified as the negative of the log(P) value. g) H3 Histone lysine 4 trimethylation (H3K4me3) coverage analyzed using CUT‐and‐TAG and h) CpG methylation patterns determined via RRBS at the same loci as in (c) in representative samples from the +ATRA and −ATRA conditions. All representative RRBS regions of interest are zoomed‐in to improve clarity in promoter regions except Tnf. Scales in (c): Foxp3 [0‐150], Rorc [0‐380], Il17a [0‐130], Il17f [0‐260], Il1r1 [0‐700], Il6ra [0‐920], Tnf [0‐900]; boxes in (c) highlight regions of apparent signal differences between +ATRA and −ATRA cells at respective gene loci; data in (d) represent the integrated ATAC signal in normalized reads across each known gene promoter region ranked as _z_‐scores using data across each row; data in (e) represent DAR _z_‐scores calculated using the average of all samples, i.e., across each row; data in (f) represent motifs with an enrichment log(P) value less than −35 found in 10% or more regions with coverage showing a fold increase of at least 1.5 over background coverage in at least one cluster; scales in (g): Foxp3 [0‐31], Rorc [0‐123], Il17a [0‐2.5], Il17f [0‐5], Il1r1 [0‐5], Il6ra [0‐72], Tnf [0‐45]; scales in h: Foxp3 [0‐70], Rorc [0‐26], Il17a [0‐26], Il17f [0‐12], Il1r1 [0‐26], Il6ra [0‐76], Tnf [0‐79].