Abstract 1453: Transcriptoma analyses in triple-negative breast cancer with BRCA1 germline mutation
Authors: Nakamura Kivvi Duarte , Ferreira Elisa , Ramalho Rodrigo , Brianese Rafael , Carraro Dirce 
Published: July 2017

Abstract
Triple-negative breast cancer (TNBC), characterized by lack of expression of the estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), is associated with a higher prevalence of germline BRCA1 mutations, especially in younger women. TNBC comprises approximately 15% of breast cancer cases and is considered one of the most aggressive subtypes. BRCA1 protein plays a pivotal role in DNA damage repair, cell cycle control and transcriptional regulation. In this context, we aimed to investigate the transcriptional difference of paired tumor and adjacent normal tissue from young patients in two TNBC groups - with or without BRCA1 germline mutation. Fourteen early-onset patients (≤41 years), with TNBC previously evaluated for BRCA1 and 2 germline mutation, were included. From these, nine patients are BRCA1/2 wild-type and five patients were BRCA1 germline mutation carriers. RNASeq libraries were constructed from rRNA depleted total RNA extracted from paired tumor and normal adjacent samples and sequenced on Illumina NextSeq 500 platform. Approximately 20 million reads aligned to human genome were generated per sample, revealing about 14,500 expressed genes with at least 10 copies per sample. Expression values were normalized by library-size read counts followed by a gene-wise normalization. To explore similarity level between samples we used the full matrix of the log2-transformed gene expression values and calculated sample-to-sample distances for each tumor compared to each normal sample, based on the Euclidian distances between samples considering all available genes. We observed that 80% of the BRCA1-mutated and 67% of the BRCA1/2 wild-type samples were clustered together. Also, we detected that BRCA1-mutated TNBC showed, in general, less difference in transcriptional pattern related to normal breast tissue than the BRCA1/2-wild type TNBC. Moreover, we compared differential expression between normal and tumor samples of each group (BRCA1-mutated and BRCA1/2-wild-type samples) using a linear-based model in DESeq2 program. Based on the criteria of fold-change ≥ │4│and FDR ≤ 0.01 we identified 2,809 DEGs, in the group of BRCA1-mutated samples, being 722 up regulated and 2,087 down regulated in the tumor and 904 DEGs in the group of BRCA1/2- wild-type samples, 399 were upregulated and 505 downregulated in the tumor. Interestingly, both lists of upregulated genes in TNBC of BRCA1-mutated and BRCA1/2-wild type were significantly enriched in the same molecular pathway involved with the cell cycle and mitosis, according to Reactome Pathways software. Overall, our first observation based on this preliminary data was that, in terms of general gene expression analysis, BRCA1-mutated TNBC has less transcriptional modification in comparison to the normal tissue than the BRCA1/2-wild type and that the tumorigenic process of both groups are similar in terms of defective biological pathway.
Citation Format: Kivvi Duarte Nakamura, Elisa Ferreira, Rodrigo Ramalho, Rafael Brianese, Dirce Carraro. Transcriptoma analyses in triple-negative breast cancer with BRCA1 germline mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1453. doi:10.1158/1538-7445.AM2017-1453