GSE128388
Gene expression changes caused by KRAS in MCF-10A
Tumor formation hinges on the acquisition of  two or more driver genes that cause normal cells  to progress from proliferation to abnormal  expansion and malignancy. In order to understand  the minimum genetic alterations involved in this  process, we compared the transcriptomes of an  isogenic set of breast epithelial cell lines that are  non-transformed, or contain a single or double  knock-in (DKI) of mutant PIK3CA (H1047R) or  KRAS (G12V). Gene set enrichment analysis  revealed that DKI cells were enriched over single  mutant cells for genes that characterize a MYC-  target gene signature. This gene signature was  mediated in part by the bromodomain-containing  protein, 9 (BRD9) that was found in the SWI-SNF  chromatin-remodeling complex, bound to the MYC  super-enhancer locus. Small molecule inhibition of  BRD9 reduced the MYC transcript and increased  the MYC-negatively regulated target, NDRG1.  Critically, only DKI cells had the capacity for  anchorage-independent growth in semi-solid  medium, and CRISPR/Cas9 manipulations showed  that PIK3CA and BRD9 expression were essential  for this phenotype. In contrast, KRAS was  necessary for DKI cell migration, and  overexpression of BRD9 partially rescued the  growth of KRAS single mutant cells in semi-solid  medium. These results provide new insight into  the earliest transforming events driven by  oncogene cooperation, and suggest BRD9 is an  important mediator of mutant PIK3CA/KRAS-  driven transformation. Overall design: MCF-10A cells were modified by knock-in of KRAS-G12V mutation in a single endogenous locus or by the combination of PIK3CA-H1047R and KRAS-G12V.  Total RNA was extracted from these cell lines and compared with existing RNAseq data of MCF-10A and MCF-10A PIK3CA-H1047R.