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Expression Patterns of SOX10 deficient BRAFi/MEKi tolerant and SOX10 KO A375 cell lines

ABSTRACT: Expression Patterns of SOX10 deficient BRAFi/MEKi tolerant and SOX10 KO A375 cell lines

PROVIDER: PRJNA748713 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15208959_1.fastq.gz	Fastqsanger.gz
	SRR15208959_2.fastq.gz	Fastqsanger.gz
	SRR15208960_1.fastq.gz	Fastqsanger.gz
	SRR15208960_2.fastq.gz	Fastqsanger.gz
	SRR15208961_1.fastq.gz	Fastqsanger.gz

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Expression Patterns of SOX10 deficient BRAFi/MEKi tolerant and SOX10 KO A375 cell lines

Project description:Given the heterogeneous expression of SOX10 in naïve melanoma, we sought to characterize SOX10 deficient population. To this end, we generated SOX10 CRISPR/Cas9 knockouts using two different guide RNAs (gRNA, #2 and #4) in the A375 (BRAF mutant) metastatic cell line. Using this approach, we identified multiple clones with loss of SOX10 expression. RNA-seq was performed to characterize the SOX10-regulated transcriptome. We used GSEA analysis to evaluate significant pathway changes in SOX10 knockout cells when compared to parental cells. We observed an enrichment in pathways associated with the tumor microenvironment (epithelial-mesenchymal transition; TGF beta signaling; extracellular structure organization; apical junction; hypoxia; angiogenesis), alterations in metabolic pathways (increase in the glycolysis pathway), a reduction in MYC and E2F targets and upregulation in p53 pathway and TNFA signaling via NFkB in the SOX10 knockout cells compared to parental cells. SOX10 negative clones have been identified in the minimal residual disease in BRAF mutant PDX models following BRAF and MEK inhibition and in patient samples while on treatment and SOX10 loss has been described as a resistant mechanism in BRAF mutant melanoma patients following vemurafenib treatment. Thus, we also analyzed the transcriptome profile of SOX10 low/deficient cells that arose following BRAFi+MEKi treatment in vivo. We performed GSEA analysis on RNA-seq data of CRT34 and CRT35 cells compared to parental A375 cells. CRT34 and CRT35 showed a very similar transcriptome profile to SOX10 KO cells when compared to A375 parental cells

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