Thompson et al89 recently reported fusion transcript analysis by five different groups from 813 breast tumors from The Cancer Genome Atlas (TCGA). Although the presence of specific recurrent fusion transcripts was low, most tumors were reported to have at least one or more fusions. ESR1-CCDC170,C20orf3-ACSS1, and USP22-MYH10 fusions were detected in ≥10 tumors in this cohort. The authors also found ERBB2 to be one among the most common 5′ and 3′ fusion partners and was seen in >10 tumors. Several other groups have focused on smaller cohorts of breast cancer cell lines and/or tumor samples and have recently reported the recurrence of specific types of fusions.90–94 Varley et al93 used RNA-seq in 28 breast cancer cell lines and identified six candidate fusion transcripts. Five of these fusion transcripts were confirmed to be present in primary human breast tumors. Comparison of matched adjacent normal tissue with fusion-positive tumor revealed that two of the fusion transcripts, SCNN1A-TNFRSF1A and CTSD-IFITM10, were highly tumor specific (Table 4). Another group investigated 14 breast cancer cell lines for the association of gene fusions to well-known chromosomal loci and reported that 60% of the gene fusions were localized to recurrent amplicons, suggesting that these fusions are a by-product of amplification.91Regarding data from cancer cell lines, it is important to note that alterations may represent those found in the original tumor or be de novo mutations arising during culture.

Several groups have identified recurrent fusions with potential clinical implications. Robinson et al92identified the presence of several recurrent gene rearrangements involving MAST and NOTCH family genes using paired-end RNA-seq in 89 cell lines and 69 breast cancer samples. They reported that these genes were repeatedly fused in ~4% and 6% of cases for MAST and NOTCH gene families, respectively. Functional studies suggesting the oncogenic potential of these fusions and of gamma secretase inhibitor in xenograft models showed reduced tumor growth for NOTCH family fusion-positive cell lines. Clinical trials with gamma secretase inhibitors are in progress for breast cancer ( Yet, most studies include unselected populations and are agnostic to NOTCH genotype, eg, mutations, fusions. Therefore, evaluation of genotype-phenotype associations may define whether these fusions are even relevant as markers for response to gamma secretase inhibitors.

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Enrichment of some fusions may also reflect specific molecular subsets of breast cancer. For instance, an integrative pipeline to probe TCGA revealed ESR1-CCDC170 fusions as a top candidate. The frequency of the rearrangement between ESR1 and its neighboring gene CCDC170 occurred in 4% of ER+ breast tumors (n = 200).95 Based on the genomic locations of these two genes and orientation of fusions observed, the authors suggest tandem duplications as the potential mechanism behind the generation of such fusions, as illustrated in Figure 2A. The role of this fusion in oncogenesis and in potentially mediating endocrine resistance is under further investigation.

(To view a larger version of Figure 2, click here.)

Other breast cancer subtypes with distinct biological behavior have been genomically evaluated using next-generation sequencing strategies. One study that sequenced TNBC samples in Mexican and Vietnamese populations reported ~7% recurrence of MAGI3-AKT3 fusion (Figure 2B).96 Expression of the fusion in a breast cancer cell line resulted in constitutive activation of the AKT3 kinase domain and downstream pathway signaling. More functional assays are required to clarify the clinical relevance of the MAGI3-AKT3 fusion and the therapeutic benefit of Akt inhibitors in fusion-positive TNBC (Table 4). Another follow-up study aimed at verifying and determining the frequency of these fusions in a larger cohort of TNBCs from Caucasian women failed to detect any MAGI3-AKT3 fusions.97 The first study performed RT-PCR of cDNA from samples followed by Sanger sequencing. The second study analyzed samples using dual color FISH probes for MAGI3 and AKT3 and did not find any signals either by fusion or break-apart probes. They also used RT-PCR for a fraction of samples and analyzed the RNA-seq data of another cohort from TCGA. While there are major differences in the methods used for detection and in cohort populations, these studies underline the importance and challenges of validation and characterization of recurrent fusions in tumors.