We introduce a classification of breast tumors into seven classes which are more clearly defined by interpretable mRNA signatures along the PAM50 gene set than the five traditional PAM50 intrinsic subtypes. Each intrinsic subtype is partially concordant with one of our classes, and the two additional classes correspond to division of the classes concordant with the Luminal B and the Normal intrinsic subtypes along expression of the Her2 gene group. Our Normal class shows similarity with the myoepithelial mammary cell phenotype, including TP63 expression (specificity: 80.8% and sensitivity: 82.8%), and exhibits the best overall survival (89.6% at 5 years). Though Luminal A tumors are traditionally considered the least aggressive, our analysis shows that only the Luminal A tumors which are now classified as myoepithelial have this phenotype, while tumors in our luminal class (concordant with Luminal A) may be more aggressive than previously thought. We also find that patients with basal tumors surviving to 48 months exhibit favorable continued survival rates when certain markers for B lymphocytes are present and poor survival rates when they are absent, which is consistent with recent findings.

我们将乳腺肿瘤分为七类，与五种传统的 PAM50 内在亚型相比，这些类别通过 PAM50 基因集的可解释 mRNA 特征更清晰地定义。每个内在亚型与我们的类别之一部分一致，并且另外两个类别对应于沿着Her2基因组的表达与Luminal B和正常内在亚型一致的类别的划分。我们的正常类别与肌上皮乳腺细胞表型相似，包括 TP63 表达（特异性：80.8%，敏感性：82.8%），并且表现出最佳的总体生存率（5 年时为 89.6%）。尽管 Luminal A 肿瘤传统上被认为是侵袭性最小的，但我们的分析表明，只有现在被分类为肌上皮的 Luminal A 肿瘤才具有这种表型，而我们的 Luminal 类肿瘤（与 Luminal A 一致）可能比之前认为的更具侵袭性。我们还发现，当存在某些 B 淋巴细胞标志物时，存活至 48 个月的基底肿瘤患者表现出良好的持续生存率，而当存在某些 B 淋巴细胞标志物时，生存率较差，这与最近的研究结果一致。