While whole-genome sequencing of tumor samples has revealed the high frequency of somatic mutations in non-coding regions, limited effort has been made to understand their oncogenic potential. To understand the impact of non-coding somatic mutations and their contribution to disease characterization, we looked for mutations affecting the promoters of genes related to the malignancy of triple-negative breast cancer (TNBC) cells.
We used gene expression data from isogenic TNBC cell lines with different metastatic abilities to identify associated changes in the activity of key regulators, resulting in 354 differentially active regulators (FDR < 0.001). With this set as a seed, we obtained a network of potential regulators of metastasis in TNBC and leveraged the presence of highly functional promoter mutations reported in TNBC patients to look for recurrently mutated subnetworks. Using a network propagation analysis, we identified the chromatin remodeler BAF (mSWI/SNF) as a protein complex overrepresented in regulatory mutations in TNBC. 
We tested the transcriptional impact of regulatory mutations affecting BAF genes using single-cell reporter assays and confirmed significant effects for mutations in the promoters of SMARCA4, SMARCC2, SMARCD2 and ARID1A (p-value < 0.001, Wilcoxon test). Finally, we are assessing the influence of the transcriptional modulation of these candidates in the malignant characteristics of TNBC cells. As a first attempt, we have diminished SMARCA4 and ARID1A levels with shRNA-mediated knock-down, and observed a decrease in stemness features in MDA-MB-231 cells. We believe this work presents an effort to explore the potential use of regulatory mutations to understand cancer progression and identify key pathways driving malignant phenotypes.