Abstract A28: Copy number and miRNA profiling in triple-negative breast cancer patients from Latin America

Abstract

Abstract Epidemiologic and molecular studies have shown that breast cancer subtypes are distributed unevenly among racial/ethnic groups. The incidence of the triple-negative breast cancer (TNBC) subtype in particular, one of the most clinically aggressive breast cancer subtypes, affects around 20% of women from Latin America, 24-28% of African-Americans, 6-8% of Asians, and around 12% of non-Hispanic Whites. In general Latin American patients with TNBC are more often diagnosed with earlier age, advanced stage, are likely to experience metastasis and be refractory to treatment. Although the characterization of the genomic profiles in each breast cancer subtype has been extensively performed, few studies have characterized them in specific ethnic groups. This translates to a deficiency in the understanding of the intrinsic characteristics of their tumors' genome, which can differentially impact their tumor phenotypes and clinical behavior. In this study we performed genome-wide array-CGH and miRNA profiling in TNBC (n=29) and non-TNBC cases (n=27) of patients from Latin America, Brazil (Curitiba-PR), to characterize their patterns of copy number and miRNA expression. These data were integrated to determine whether the location of miRNAs in genomic regions rich in copy number alterations (CNAs) could impact their expression levels and whether there were common miRNA target genes affected by both CNAs and miRNA deregulation. Our findings showed a distinct pattern of CNAs and miRNA expression between the TNBC and non-TNBC cases. A total number of 309 and 124 CNAs were identified in the TNBC and non-TNBC cases, with an average of 10.65 and 7.75 CNAs per case, respectively. In the TNBC cases, the most frequent (>30% of the cases) cytobands affected by CNAs were 8q11.21-q24.3, 1q21.1-q44, 7q11.23-q36.3, 12p13.33-p11.1, 3q11.2-q29, and 6p25.3-p11.2. MiRNA profiling analysis showed 209 miRNAs with significant differentially expression between these two groups (P<0.05; FDR<0.05): 108 and 101 with up- and downregulated expression, respectively. The mapping of these 209 miRNAs in regions with CNAs in the same TNBC cases led to the identification of a panel of 27 miRNAs, 12 of which (miRs-544b, 567, 568, 586, 592, 610, 634, 668, 802, 944, 1260, and 3161) with miRNAs expression concordant with CNAs. Area Under the Curve (AUC) value >0.7 was observed for 75% of these miRNAs; miRs-567, 610, 802, 944 and 1260a presented the highest discriminatory power, with AUC values >0.8. A number of 1312 genes were identified mapped in the most common CNAs and targeted by these miRNAs. Subsequent pathway analysis of the 12 miRNAs showed their involvement in cancer-related pathways, including the Hippo, TGF-beta, and Ras signaling pathways; a close hierarchical cluster was observed with the miRs-592, 634, 802, 944, and 1260 in regulating these pathways. In conclusion, the TNBC and non-TNBC cases of the patients of this study presented a distinct pattern of CNAs and miRNA expression levels. The copy number and miRNA integrated analysis performed delineated the boundaries of genomic instability regions and the mapping of the most relevant miRNA targets in these TNBC cases, that can act as potential oncogenes and/or tumor suppressor genes in these regions. These findings contributed to the identification of unique ethnic miRNA/mRNA pairings and their corresponding cancer signaling pathways that are of relevance to the TNBC of Latin American patients and that can be directly and more efficiently targeted for therapy. Support: Georgetown University Center of Excellence in Regulatory Science and Innovation (CERSI U01FD004319), a collaborative effort between the university and the U.S. Food and Drug Administration. This research does not necessarily reflect the views of the FDA. The authors thank CNPq and CAPES, Brazil, for scholarships (B.S., S.R.P.). Note: This abstract was not presented at the conference. Citation Format: Bruna Sugita, Silma R. Pereira, Rodrigo Almeida, Rubens S. Lima, Cicero A. Urban, Simina Boca, Yuriy Gusev, Iglenir J. Cavalli, E.M.S.F. Ribeiro, Luciane R. Cavalli. Copy number and miRNA profiling in triple-negative breast cancer patients from Latin America [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A28.