Abstract
Basal-like breast cancer is an aggressive subtype generally characterized as poor prognosis and lacking the expression of the three most important clinical biomarkers, estrogen receptor, progesterone receptor, and HER2. Cell lines serve as useful model systems to study cancer biology in vitro and in vivo. We performed mutational profiling of six basal-like breast cancer cell lines (HCC38, HCC1143, HCC1187, HCC1395, HCC1954, and HCC1937) and their matched normal lymphocyte DNA using targeted capture and next-generation sequencing of 1,237 cancer-associated genes, including all exons, UTRs and upstream flanking regions. In total, 658 somatic variants were identified, of which 378 were non-silent (average 63 per cell line, range 37–146) and 315 were novel (not present in the Catalogue of Somatic Mutations in Cancer database; COSMIC). 125 novel mutations were confirmed by Sanger sequencing (59 exonic, 48 3’UTR and 10 5’UTR, 1 splicing), with a validation rate of 94% of high confidence variants. Of 36 mutations previously reported for these cell lines but not detected in our exome data, 36% could not be detected by Sanger sequencing. The base replacements C/G>A/T, C/G>G/C, C/G>T/A and A/T>G/C were significantly more frequent in the coding regions compared to the non-coding regions (OR 3.2, 95% CI 2.0–5.3, P<0.0001; OR 4.3, 95% CI 2.9–6.6, P<0.0001; OR 2.4, 95% CI 1.8–3.1, P<0.0001; OR 1.8, 95% CI 1.2–2.7, P = 0.024, respectively). The single nucleotide variants within the context of T[C]T/A[G]A and T[C]A/T[G]A were more frequent in the coding than in the non-coding regions (OR 3.7, 95% CI 2.2–6.1, P<0.0001; OR 3.8, 95% CI 2.0–7.2, P = 0.001, respectively). Copy number estimations were derived from the targeted regions and correlated well to Affymetrix SNP array copy number data (Pearson correlation 0.82 to 0.96 for all compared cell lines; P<0.0001). These mutation calls across 1,237 cancer-associated genes and identification of novel variants will aid in the design and interpretation of biological experiments using these six basal-like breast cancer cell lines.
Highlights
Among women, breast cancer is the most common malignancy and a leading cause of death with nearly 1.7 million cases diagnosed worldwide and over 500 thousand deaths every year [1]
The vast majority of breast cancers result from mutations acquired by aging and lifestyle and environmental factors acting in combination with genetic predisposition [6, 7]
Molecular characterization has shown that breast cancer is a highly heterogeneous disease that can be divided into at least four well-defined subtypes: the hormone receptor positive subtypes, luminal A and luminal B, the HER2 subtype enriched for cases with HER2 amplification, and the basal-like subtype which usually lacks expression of the estrogen (ER), progesterone (PR), and HER2 receptors [8,9,10]
Summary
Breast cancer is the most common malignancy and a leading cause of death with nearly 1.7 million cases diagnosed worldwide and over 500 thousand deaths every year [1]. A minority of these cases, 5–10%, are caused by mutations in high-penetrance germline loss-of function genes (BRCA1, BRCA2) or in low-penetrance susceptibility genes/regions, not all of the hereditary genetic factors have been identified [2,3,4,5]. Molecular characterization has shown that breast cancer is a highly heterogeneous disease that can be divided into at least four well-defined subtypes: the hormone receptor positive subtypes, luminal A and luminal B, the HER2 subtype enriched for cases with HER2 amplification, and the basal-like subtype which usually lacks expression of the estrogen (ER), progesterone (PR), and HER2 receptors (so called “triple-negative”) [8,9,10]. Hereditary BRCA1-mutations appears to primarily predispose for the development of basal-like breast cancers [13], indicating that BRCA1 dysfunction is a potent driver of basal-like tumorigenesis. There is a great demand for an improved understanding of basal-like breast cancer biology and for the development of drug targets for this aggressive subtype
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