DrugMap: A quantitative pan-cancer analysis of cysteine ligandability (RNA-Seq)

SOX10 is a lineage-restricted transcription factor important for melanoma proliferation and survival. Our data demonstrate that SOX10 genetic depletion by CRISPR/Cas9 significantly impaired melanoma proliferation. We chose 7 different melanoma, all of which exhibited growth dependency on SOX10 with different levels. To define the SOX10 transcriptional signature shared with different SOX10-dependent melanoma, we performed bulk RNA-seq on 7 melanoma transfected with siSOX10 or siControl. Each melanoma cell line was plated and transfected with each siRNA to deplete SOX10 protein expression. After 72 hrs, cells were lysed with Buffer TCL(QIAGEN) supplemented with 2-ME and stored at -80C until use. Libraries from each cell line were made with the modified Smart-seq2 protocol. Each replicate was uniquely barcoded and all the samples were pooled for sequencing. (2) We developed a chemical probe (SH-0029) that covalently engages SOX10. To examine the effect of SH-0029 on SOX10 target genes, SOX10-dependent SKMEL5 melanoma were plated and treated with SH-0029, SH-0105 (a control probe), or DMSO(vehicle) for 48h. Total RNA was extracted with NucleoSpin RNA extraction kit (MACHEREY-NAGEL) and mRNA was subsequently purified with poly dT-attached magnetic beads. We found that downregulated genes induced by SH-0029 treatment strongly overlapped with those by SOX10 genetic depletion, suggesting that SOX10 covalent ligand controls SOX10 transcriptional network.