Next-generation sequencing identifies recurrent copy number variations in invasive breast carcinomas from Ghana.

ABSTRACT

African and African-American (AA) women have higher incidence of triple-negative breast cancers (TNBC) with high histological grade and aggressive clinical behavior, but the reasons are not fully understood. We recently found that the oncogenic protein EZH2 is overexpressed in Ghanaian breast cancer patients, with 16% of the tumors expressing cytoplasmic EZH2. Understanding the molecular underpinnings of these aggressive tumors may lead to the identification of potential targetable oncogenic drivers. We characterized the copy number variations of 11 Ghanaian breast tumor patients by targeted multiplexed PCR-based DNA next-generation sequencing (NGS) over 130 cancer-relevant genes. While the DNA quality was not optimal for mutation analysis, 90% of the tumors had frequent recurrent copy number alterations (CNAs) of 17 genes SDHC, RECQL4, TFE3, BCL11A, BCL2L1, PDGFRA, DEK, SMUG1, AKT3, SMARCA4, VHL, KLF6, CCNE1, G6PD, FGF3, ABL1, and CCND1, with the top oncogenic functions being mitotic G1-G1/S-phase regulation, gene transcription, apoptosis, and PI3K/AKT pathway. The most common recurrent high-level CNAs were gains of RECQL4 and SDHC, in 50% and 60% of cases, respectively. Network analyses revealed a significant predicted interaction among 12 of the 17 (70.6%) genes with high-level CNAs (p = 5.7E-07), which was highly correlated with EZH2 expression (r = 0.4-0.75). By immunohistochemistry, RECQL4 and SDHC proteins were upregulated in 53 of 86 (61.6%) and 48 of 86 (56%) of Ghanaian invasive carcinoma tissue samples. In conclusion, our data show that invasive carcinomas from Ghana exhibit recurrent CNAs in 17 genes, with functions in oncogenic pathways, including PI3K/AKT and G1-G1/S regulation, which may have implications for the biology and treatment of invasive carcinomas in African and AA women.