Comparison of GATA3 mutant and GATA3 wild type isogenic MCF-7 and CAMA1 breast cancer cell lines

The GATA3 transcription factor is one of the most frequently mutated genes in breast cancer. Heterozygous mutations, largely frameshifting, are seen in 15% of estrogen receptor positive breast cancers, the subtype in which these mutations are almost exclusively found. Mouse studies have shown that Gata3 is critical for breast development and that GATA3 gene dosage affects breast tumor progression. Human patient data have shown that high Gata3 expression, a feature of luminal subtype breast cancers, is associated with a better prognosis. Although the frequency of GATA3 mutation suggests an important role in breast cancer development or progression, there is little understanding of how mutations in GATA3 affect its function in luminal breast epithelial cells and what gene expression changes result as a consequence of the mutations. Here, using gene editing, we have created two sets of isogenic human luminal breast cancer cell lines with and without a truncating GATA3 mutation. GATA3 mutation enhanced tumor growth in vivo but did not affect sensitivity to clinically used hormonal therapies or chemotherapeutic agents. We identified genes upregulated and downregulated in GATA3 mutant cells, a subset of which was concordantly differentially expressed in GATA3 mutant primary luminal breast cancers. Addback of mutant GATA3 recapitulated mutation-specific gene expression changes and enhanced soft agar colony formation, suggesting a gain of function for the mutant protein. Parental MCF-7 cells with endogenous heterozygous GATA3 D336fs*17 mutation are compared to two independently derived gene-edited GATA3 wild type clones. Biological replicates (independent cultures and RNA preparations) were run and array analysis was performed on two separate occasions using independent samples from these three cell lines. A separate comparison was performed between CAMA1 breast cancer cells and a single gene-edited clone with knock-in of the GATA3 D336fs*17 mutation on a single allele. Single replicates were compared for these CAMA1 and GATA3 mutant samples.