Abstract 2788: Comprehensive high-depth target sequencing in circulating tumor DNAs of patients with inflammatory and non-inflammation breast cancers
Authors: Yang Hushan , Zhong Xue , Wei Qiang , Mu Zhaomei , Ye Zhong , Lai Yinzhi , Lin Huei-Wen , Jaslow Rebecca , Avery Tiffany , Austin Laura , Sun Zhaohui , Lin Shengrong , Zhao Grace , Tang Ling Fang , Myers Ronald E. , Palazzo Juan P. , Biederman Laura , Li Bingshan , Cristofanilli Massimo 
Published: August 2015

Abstract
Inflammatory breast cancer (IBC) is an extremely aggressive form of locally advanced breast cancer that affects about 5% of breast cancer patients. The prognosis of IBC patients is remarkably poor, with a three-year survival rate of approximately 30% compared to 60% for patients with non-IBC breast cancers. These facts highlight the importance of accurate characterization, early detection, and timely treatment of IBC patients. Thus, it is important to develop novel and clinically applicable non-invasive biomarkers to characterize the unique presentation of IBC. In this study, we searched for somatic mutations in the circulating tumor DNAs (ctDNAs) that could be used to non-invasively characterize IBC patients and inform their clinical management. Using ctDNAs extracted from plasma of 10 pairs of IBC and non-IBC patients that were matched on major demographic and clinical variables, we conducted a high-depth target next-generation sequencing study that interrogated a comprehensive panel of 127 TCGA (The Cancer Genome Atlas)-reported cancer-related genes with &gt;7000 uniquely designed and validated probes. Overall, we obtained &gt;500x coverage in &gt;80% of the interrogated regions, and &gt;100x coverage in &gt;97% of the regions. We found that C&gt;T mutations predominated in well-reported mutated genes such as TP53, PIK3CA, EGFR, and CDH1. Compared to non-IBC patients, IBC patients appeared to have a higher percentage of mutations in PIK3CA but a lower percentage in TP53. Interestingly, about 78% of mutated genes that were only detected in IBC patients encode zinc finger-related proteins, a family of transcriptional factors that have been implicated in IBC development. In comparison, about 43% of genes that were detected only in non-IBC patients encode proteins important to cell division regulation. Furthermore, network-based stratification (NBS) analysis of the mutation profile revealed clusters of IBC relative to non-IBC samples, indicating the potential of mutation profiling in identifying molecularly distinct subtypes of IBC patients. Preliminary longitudinal analysis of ctDNAs from three patients with multiple plasma samples indicated that de novo mutations in important genes including PIK3CA, RB1, and KRAS appeared in patient blood after chemotherapy and/or targeted therapy treatments. Moreover, the emergence of some of these mutations was temporally correlated with the responses of patients to the treatments they received. Overall, this study provides novel evidence that ctDNA mutation status may help to non-invasively characterize IBC tumors, and might also serve as a novel non-invasive marker to monitor treatment efficacy and prognosis of breast cancer patients. Future studies with larger sample sizes are warranted to confirm our findings and identify additional clinically useful markers for the characterization and management of IBC and non-IBC patients.
Citation Format: Hushan Yang, Xue Zhong, Qiang Wei, Zhaomei Mu, Zhong Ye, Yinzhi Lai, Huei-Wen Lin, Rebecca Jaslow, Tiffany Avery, Laura Austin, Zhaohui Sun, Shengrong Lin, Grace Zhao, Ling Fang Tang, Ronald E. Myers, Juan P. Palazzo, Laura Biederman, Bingshan Li, Massimo Cristofanilli. Comprehensive high-depth target sequencing in circulating tumor DNAs of patients with inflammatory and non-inflammation breast cancers. [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 2788. doi:10.1158/1538-7445.AM2015-2788