Fig. 1: Three-dimensional epigenomic profiling reveals altered super-enhancer engagement in multiple myeloma. | Nature Communications

Fig. 1: Three-dimensional epigenomic profiling reveals altered super-enhancer engagement in multiple myeloma.

From: Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma

Fig. 1

a Heatmap showing H3K27ac enrichment patterns in different clusters of SE across NPC (n = 1), MBC (n = 3), B-lymphoma cell lines (n = 2), HMCLs (n = 9), and MM patient samples (n = 19). Each column represents a sample, which are color-coded by the corresponding sample group (NPC, MBC, B-lymphoma, HMCL, and primary MM). The clusters and the number of SEs specific to each cluster are indicated on the left. b GREAT analysis of genes linked to MM-associated enhancers, showing enriched pathway terms curated from the Molecular Signatures Database (MSigDB). P values were calculated using one-sided Fisher’s exact test and were adjusted using the Benjamini-Hochberg method. c GO enrichment analysis of genes associated with acquired SEs in MM. Each GO category (BP, CC, MF) is shown. P values were calculated using one-sided Fisher’s exact test and were adjusted using the Benjamini-Hochberg method. d Heatmaps illustrating the H3K4me1, H3K4me3, H3K9me3, H3K27ac and H3K36me3 ChIP-seq and RNA-seq patterns from the Blueprint database34,35,36,37,54 at the candidate MM SE-associated genes (top panel) and MM-associated SEs (bottom panel) in patient-derived myeloma cells (n = 4) compared to NPCs (n = 2). RNA-seq data (FPKM) is available for three myeloma samples and one NPC sample only. Samples are organized by hierarchical clustering, with labels colored in gray and black highlighting MM patient and normal control samples, respectively. e Schematic representation of the workflow utilized to discover target genes driven by MM SEs and associated with potential clinical relevance. The number of samples or candidate genes is indicated in brackets. The nine prioritized candidate genes that have been characterized in MM are labeled in blue, and other genes are labeled in red. Figure 1 created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license. BP biological process, CC cellular component, MF molecular function.

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