Abstract 1119: Subclonal structure of breast cancer subtypes determined by quantitative analyses of activating mutations

Little is known about the role of low-frequency somatic mutations in breast cancer, a cancer that is quite variable in terms of clinical features, prognosis and response to treatment. Because undetected mutant subpopulations have the potential to cause resistance to molecularly-targeted cancer therapies, this study investigated whether different subtypes of ductal carcinomas (DCs) encompass subpopulations of cells with cancer-driver mutations known to impact response to targeted therapies. Using the sensitive and quantitative ACB-PCR approach PIK3CA H1047R and BRAF V600E point mutations were quantified in 82 DCs, consisting of ER/PR+/HER2- (n = 20), ER/PR+/HER2+ (n = 20), ER/PR-/HER2+ (n = 21), and ER/PR-/HER2- (TNBC; n = 21) subtypes. Considering all subtypes together, the geometric mean mutant fraction (MF) measurements [provided along with (5 th to 95 th percentiles)] were: PIK3CA H1047R, 6.8 × 10 −6 (2.5 × 10 −8 to 6.3 × 10 −2 ) and BRAF V600E, 1.9 × 10 −5 (5.1 × 10 −6 to 1.6 × 10 −4 ). The PIK3CA H1047R and BRAF V600E mutations were detected (i.e., had MFs > 10 −5 ) in 41% and 37% of DCs, respectively. In addition, normal breast tissues were analyzed by ACB-PCR to define the background levels of these mutations. For normal breast (n = 10), the geometric mean MF measurements [provided along with (5 th to 95 th percentiles)] were: PIK3CA H1047R, 8.0 × 10 −4 (1.6 × 10 −5 to 3.8 × 10 −2 ) and BRAF V600E, 2.0 × 10 −6 (9.7 × 10 −7 to 1.7 × 10 −4 ). DC subtype analyses revealed ER/PR+/HER2- and TNBC subtypes had significantly greater BRAF V600E MFs relative to that measured in normal breast. The ACB-PCR data indicated 15% of DCs carry BRAF V600E mutation at a level greater than the upper 95% confidence interval for the mutation in normal breast. Interestingly, for PIK3CA H1047R mutation, ER/PR+/HER2-, ER/PR+/HER2+ and TNBC subtypes had significantly less PIK3CA H1047R mutation relative to that measured in normal breast. We hypothesize that pre-existing PIK3CA mutation can cooperate with other clones to drive tumor initiation and early progression, but is lost or outgrown by clones carrying other cancer driver mutations in advanced breast cancers. Data from the COSMIC database supports this idea that the level of PIK3CA mutation decreases as disease progression ensues, with PIK3CA mutation detected in 47% of hyperplasia, 29% of DCIS, and 21% in ductal carcinomas. Furthermore, TNBCs had significantly less PIK3CA H1047R mutation relative to that measured in each of the other subtypes, suggesting individuals with these tumors may have a lower response to inhibitors of the PI3K/AKT/mTOR pathway. Analyses of other cancer driver hotspot point mutations in the different DC subtypes is ongoing and will provide additional information regarding the role of low-frequency somatic mutations in breast cancer. Citation Format: Meagan B. Myers, Malathi Banda, Karen L. McKim, Barbara L. Parsons. Subclonal structure of breast cancer subtypes determined by quantitative analyses of activating mutations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1119. doi:10.1158/1538-7445.AM2015-1119