Fig. 3: Ectopic Expression of Bmal1 Induces Sox10high YUMM2.1 Cells toward Sox9high More Mesenchymal Cell State.
From: Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity
a–f Analyses of RNA-seq data from YUMM2.1 EV, WT-Bmal1 and dHLH-Bmal1 cells. BR of 2. a Heatmap for all genes that are affected by WT-Bmal1 and dHLH-Bmal1 in the same direction versus EV in YUMM2.1. GSEA showing significantly enriched epithelial mesenchymal transition (EMT) gene set in YUMM2.1 WT-Bmal1 vs EV (b) and YUMM2.1 dHLH-Bmal1 vs EV (c). Adjust p-value by one-sided Fisher’s exact test which applied to all GSEA unless noted. d Expression of Sox9 and Sox10 mRNA level. e Transcription factor motif enrichment among 542 genes that progressively increased from YUMM2.1 EV to WT-Bmal1 and to dHLH-Bmal1 cells shown in Fig. 3a. Adjust p-value by one-sided Fisher’s exact test which applied to all transcription factor motif enrichment analysis unless noted. f Heatmap of AP-1 factors. g Immunoblot for Bmal1 and AP-1 factors in YUMM2.1 with EV, WT-Bmal1 and dHLH-Bmal1. Numbers underneath the rows represent relative expression of proteins on different gels but from the same experiment. RE of 3. h–j H3K27Ac ChIP-seq analysis of YUMM2.1 WT-Bmal1 and YUMM2.1 dHLH-Bmal1 versus YUMM2.1 EV. BR of 2. Gain or loss of H3K27Ac signals in YUMM2.1 cells with WT-Bmal1 and dHLH-Bmal1 versus EV (h). Prevalence of bZIP (AP-1) motif in all 1187 regions (i) and 131 intergenic regions (>20 kb from TSS) (j). Nominal p-value by one-sided hypergeometrical test. k H3K4me3 and H3K27Ac alterations at Sox9 and Sox10 loci in YUMM2.1 cells with WT-Bmal1 and dHLH-Bmal1 versus EV. BR of 2. l CyCIF for Sox9 (green) and Sox10 (Blue) on tissue microarray of independent tumors from YUMM2.1 EV, WT-Bma1 and dHLH-Bmal1 tumors in C57BL/6 mice. Each circular section was from a different tumor. Source data for CyCIF as Minerva story available at www.cycif.org/data/zhang-2023. m Percentage of tumor cells positive for Sox10 and Sox9 respectively in YUMM2.1 EV, WT-Bmal1 or dHLH-Bmal1 tumor tissues determined by CyCIF. Each dot represents one tumor tissue (n = 2). BR = biological replicate, RE = replicate experiment. Source data are provided as a Source Data file.
