SOX4 and SMARCA4 cooperatively regulate PI3K signaling through transcriptional activation OF TGFBR2 in triple negative breast cancer

Genomic and proteomic analyses coupled withmechanistic studies identified TGFBR2as a direct transcriptional target of SOX4and demonstrated that TGFBR2 is required to mediate SOX4-dependent PI3K signaling. We further reportthat SOX4 and the SWI/SNF ATPase SMARCA4, which are uniformly overexpressed in basal-like tumors,form a previously unreported complex that is requiredto maintain an open chromatin conformationat the TGFBR2regulatory regionsin order tomediateTGFBR2expressionand PI3K signaling. Overall design: Total RNA was extracted from HCC1143 cells treated with either siRNA targeting SOX4 or non-targeting control siRNA for 96 hours. RNA libraries were prepared using theNuGen Ovation Universal RNA-Seq System (Catalog # 0343-32)and paired end (2x48bp) sequencing was performed usingthe Illumina NextSeq system. Paired-end FASTQ files were processed using default parameters of Kallisto version v0.43.1, with 100 bootstraps for the expectation-maximization algorithm. Kallisto transcriptome index was built using the Ensembl human genome reference build 38. Gene level summarization of Kallisto abundance (TPM) was established using the R package Tximport v1.0.3 and R v3.3.1.