Genetic alterations of triple negative breast cancer by targeted next-generation sequencing and correlation with tumor morphology

Abstract

Triple negative breast cancer represents a heterogeneous group of breast carcinomas, both at the histologic and genetic level. While recent molecular studies have comprehensively characterized the genetic landscape of these tumors, few have integrated a detailed histologic examination into the analysis. In this study, we defined the genetic alterations in 39 triple negative breast cancers using a high-depth targeted massively parallel sequencing assay and correlated the findings with a detailed morphologic analysis. We obtained representative frozen tissue of primary triple negative breast cancers from patients treated at our institution between 2002 and 2010. We characterized tumors according to their histologic subtype and morphologic features. DNA was extracted from paired frozen primary tumor and normal tissue samples and was subjected to a targeted massively parallel sequencing platform comprising 229 cancer associated genes common across all experiments. The average number of non-synonymous mutations was 3 (range 0–10) per case. The most frequent somatic alterations were mutations in TP53 (74%) and PIK3CA (10%) and MYC amplifications (26%). Triple negative breast cancers with apocrine differentiation less frequently harbored TP53 mutations (25%) and MYC gains (0%), and displayed a high mutation frequency in PIK3CA and other PI3K signaling pathway related genes (75%). Using a targeted massively parallel sequencing platform, we identified the key somatic genetic alterations previously reported in triple negative breast cancers. Furthermore, our findings show that triple negative breast cancers with apocrine differentiation constitute a distinct subset, characterized by a high frequency of PI3K pathway alterations similar to luminal subtypes of breast cancer.

Insights into Molecular Classifications of Triple-Negative Breast Cancer: Improving Patient Selection for Treatment

“…Cancers harbor numerous somatic genetic alterations, though only a small proportion of them confer clear fitness advantage, also known as "cancer drivers" (35). Large-scale exome and targeted sequencing studies in primary breast tumors have revealed the presence of many alterations in putative cancer-driver genes in TNBC (36)(37)(38). The average mutation rate in basal-like breast cancer is among the highest in breast tumors, 1.68 mutations per megabase (Mb); tumors that reach rates greater than three standard deviations above the mean (>4.68 mutations/Mb) are considered hypermutated (36).…”

Apocrine lesions of the breast: part 2 of a two-part review. Invasive apocrine carcinoma, the molecular apocrine signature and utility of immunohistochemistry in the diagnosis of apocrine lesions of the breast

“…TNBC with morphologic apocrine differentiation and/or AR IHC positivity harbour a higher rate of PIK3CA and other PI3K gene mutations37–39 but a lower rate of TP53 mutations and MYC gains compared with other TNBCs38 suggesting that these tumours may also be sensitive to the PI3K pathway and cyclin-dependent kinases 4 and 6 (CDK4/6) inhibitors. Using a fluorescent CDK2 activity reporter for single cell analysis together with time-lapse imaging to test a panel of cell lines representative of TNBC (including an MDA-MB-453 LAR cell line xenograft), Asghar et al 40 have recently demonstrated that the LAR subset of TNBC proved highly sensitive to CDK4/6 inhibition both in vivo and in vitro.…”

TP53 mutations and SNPs as prognostic and predictive factors in patients with breast cancer (Review)

“…Tumors with TP53 mutations are more likely to be aggressive (triple-negative or HER-2-positive breast cancer) (8,9). TP53 mutations occur at an increased frequency in triple-negative breast cancer in comparison with non-triple-negative cancers (10,11). Furthermore, TP53 mutations have been indicated to be associated with chemoresistance (10,12,13).…”