Fig. 3
IGFBP2 is a SIRT6 target that is upregulated in MAPKi melanoma resistance. a Schematic of the integrated transcriptional profiling of MAPKi (left) on SKMel-239 L-C-B or SIRT6.2–7 and the SIRT6 regulatory network in the absence (middle) or presence (right) of MAPKi. 2178 shared downregulated genes were identified as MAPKi-sensitive genes; 864 upregulated genes were identified in SIRT6.2–7 cells; 222 shared upregulated genes upon MAPKi treatment in SIRT6.2–7 cells. Twenty genes identified as potential targets are shown in the bracket. b Haploinsufficiency of SIRT6 increases IGFBP2 expression. Log2 fold change from RNA-seq for IGFBP2 (top); blue: L-C-B with the indicated drugs or DMSO; black: DMSO-treated cells; purple: SIRT6.2–7 or SIRT6.1-1 with the indicated drugs. IGFBP2 protein expression after 4 days of 2 µM of BRAFi or 100 nM BRAFi + 1 nM MEKi in the indicated CRISPR cell lines by RPPA analysis (middle), represented by heatmap (Normalized Log2 Median Centered is shown) and by immunoblot (bottom). GAPDH was used as a loading control. c SIRT6, H3K9ac, and H3K56ac ChIP-seq meta-profiles in L-C-B cells at SIRT6-associated promoters. Plot represents average read counts per 10 bp bins. d ChIP-seq meta-profiles for SIRT6 in L-C-B, SIRT6.2–7, and SIRT6.1-1 cell lines at SIRT6-associated promoters. Upper left quadrant shows zoom in for SIRT6 signal in SIRT6.2–7 and SIRT6.1-1 at SIRT6-bound promoters. Plot represents average read counts per 10 bp bins. e Venn diagram displaying SIRT6-occupied genes at TSSs (transcription start sites) associated with increased H3K56ac in SIRT6.2–7 cells. 399 TSS show an increase in H3K56ac in SIRT6.2–7 cells and 201 SIRT6-bound TSS show an increase at H3K56ac in SIRT6.2–7 cells compared to L-C-B. 23 SIRT6-bound TSS show an increase for H3K56ac and are upregulated in SIRT6.2–7 vs. L-C-B (top). Venn diagram displaying SIRT6 targets identified by integrating transcriptomic and genomic analyses (bottom). f Capture of the UCSC (GRCh37/hg19) genome browser showing the IGFBP2 locus. L-C-B (black), SIRT6.2–7 (red), and SIRT6.1-1 (blue) ATAC-seq and ChIP-seq profiles for H3K4me1, H3K27ac, H3K4me3, H3K9ac, H3K56ac, and SIRT6 are shown (Reads Per Kilobase per Million reads). Genomic coordinates shown on top and IGFBP2 locus on bottom
