Abstract P2-03-04: Comparative analysis of somatic mutations in matched primary vs metastatic triple-negative breast cancers
Authors: Cherni Irene , Levin Maren K , O"Shaughnessy Joyce A , Carpten John D 
Published: May 2015

Abstract
Background. Treatment of triple-negative breast cancer (TNBC) is clinically challenging due to disease heterogeneity and aggressiveness which often result in high recurrence and mortality rates. We have previously reported on genomic alterations found in 14 metastatic TNBC tumors (Craig et al 2012) uncovered through whole-genome and transcriptome sequencing and found that majority of tumor changes in our cohort converged on RAS/RAF/MEK/ERK and PI3K/AKT/mTOR pathways revealing potential therapeutic targets. In this study, we interrogated patients’ matched primary and metastatic cancers using exome sequencing. Differentiating between primary and metastasis-specific genomic alterations will further our understanding of TNBC recurrence.
Methods. Tumor tissue was microdissected from 10uM FFPE sections from primary tumors of nine TNBC patients. DNA was extracted using Qiagen AllPrep kit. Whole-genome libraries were prepared from &gt;250ng of DNA using Kapa-on–Bead method. Exomes were captured using All Exon V5 capture kit (Agilent Technologies) and sequenced on Illumina HiSeq. List of somatic variants (SNVs) in primary tissue was generated using Seurat variant caller and manually compared with the SNVs uncovered previously in metastatic tumors. Presence (or absence) of all reported somatic SNVs was visually confirmed in IGV genome viewer.
Results. Our analysis revealed the majority of somatic mutations found in metastatic lesions were also present in the primary tissue (64.3% on average). Patient TNBC03 had an unusually high number of new mutations in the lung metastatic lesion (72.7%). All TP53 mutations in our cohort were an early event present in both primary and metastatic tissues. In patient TNBC01, acquired mutation in NF1 - an upstream negative regulator of RAS pathway - in addition to pre-existing PTEN deletion, CTNNA1 underexpression and RB1 mutation - suggests RAS pathway addiction which could have been responsible for disease recurrence in this patient. Interestingly, NEDD4 mutation was found in a lung metastasis of another patient whose disease was refractory to BEZ235 (PI3K/mTOR inhibitor) treatment. NEDD4 has recently been shown to be an upstream regulator of the PI3K pathway and a possible therapeutic target in cancers with downregulated PTEN. Additional select acquired mutations in metastatic lesions of our cohort included FGF14, ABCB10, MDM2, KIF1C, ATAD2B, PTPLAD2, MDM20, TDRD1, and USP6. Mutated CDH5 was found in metastases in 2 of 9 patients.
Conclusion. Our findings demonstrate the complexity and variability in somatic events underlying TNBC recurrence, reinforcing the need to re-biopsy metastatic TNBC lesions and to employ combination targeted therapies wherever possible.
Citation Format: Irene Cherni, Maren K Levin, Joyce A O"Shaughnessy, John D Carpten. Comparative analysis of somatic mutations in matched primary vs metastatic triple-negative breast cancers [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-04.