Department of Pathology, College of Medicine, University of Illinois at Chicago, 840 S. Wood Street, MC 847, Chicago, IL, 60612, USA.
Division of Epidemiology and Biostatistics, School of Public Health, University of Illlinois at Chicago, 1603 W. Taylor Street, MC 923, Chicago, IL, 60612, USA.
BMC Cancer. 2019 Mar 8;19(1):215. doi: 10.1186/s12885-019-5392-z.
PAM50 gene profiling assigns each cancer to a single intrinsic subtype. However, individual cancers vary in their adherence to a prototype, and due to bulk tissue sampling, some may exhibit expression patterns that indicate intra-tumor admixture of multiple subtypes. Our objective was to develop admixture metrics from PAM50 gene expression profiles in order to stratify Luminal A (LumA) cases according to their degree of subtype admixture, and then relate such admixture to clinical and molecular variables.
We re-constructed scaled, normalized PAM50 profiles for 1980 cases (674 LumA) in the METABRIC cohort and for each case computed its Mahalanobis (M-) distance from its assigned centroid and M-distance from all other centroids. We used t-SNE plots to visualize overlaps in subtype clustering. With Normal-like cases excluded, we developed two metrics: Median Distance Criteria (MDC) classified pure cases as those located within the 50th percentile of the LumA centroid and > =50th percentile from any other centroid. Distance Ratio Criteria (DRC) was computed as the ratio of M-distances from the LumA centroid to the nearest non-assigned centroid. Pure and admixed LumA cases were compared on clinical/molecular traits. TCGA LumA cases (n = 509) provided independent validation.
Compared to pure cases in METABRIC, admixed ones had older age at diagnosis, larger tumor size, and higher grade and stage. These associations were stronger for the DRC metric compared to MDC. Admixed cases were associated with HER2 gain, high proliferation, higher PAM50 recurrence scores, more frequent TP53 mutation, and less frequent PIK3CA mutation. Similar results were observed in the TCGA validation cohort, which also showed a positive association between admixture and number of clonal populations estimated by PyClone. LumA-LumB confusion predominated, but other combinations were also present. Degree of admixture was associated with overall survival in both cohorts, as was disease-free survival in TCGA, independent of age, grade and stage (HR = 2.85, Tertile 3 vs.1).
Luminal A breast cancers subgrouped based on PAM50 subtype purity support the hypothesis that admixed cases have worse clinical features and survival. Future analyses will explore more extensive genomic metrics for admixture and their spatial significance within a single tumor.
PAM50 基因分析将每种癌症分配到一个单一的固有亚型。然而，个别癌症在其对原型的依从性上存在差异，并且由于采用了批量组织采样，因此某些癌症可能表现出表明肿瘤内多种亚型混合的表达模式。我们的目的是从 PAM50 基因表达谱中开发混合度量标准，以便根据其亚型混合程度对 Luminal A (LumA) 病例进行分层，然后将这种混合与临床和分子变量相关联。
我们对 METABRIC 队列中的 1980 例（674 例 LumA）重新构建了经过缩放和归一化的 PAM50 图谱，并为每个病例计算了其与分配的质心的马氏（M-）距离以及与所有其他质心的 M-距离。我们使用 t-SNE 图来可视化亚型聚类中的重叠。排除正常样例后，我们开发了两个度量标准：中位数距离标准（MDC）将纯病例分类为位于 LumA 质心的第 50 个百分位数内且距离任何其他质心的距离大于等于第 50 个百分位数的病例。距离比标准（DRC）是 LumA 质心与最近非分配质心的 M-距离之比计算得出的。对临床/分子特征进行纯和混合 LumA 病例的比较。TCGA LumA 病例（n=509）提供了独立验证。
与 METABRIC 中的纯病例相比，混合病例的诊断年龄较大，肿瘤较大，分级和分期较高。与 MDC 相比，DRC 度量标准的这些关联更强。混合病例与 HER2 增益、高增殖、较高的 PAM50 复发评分、更频繁的 TP53 突变和较少的 PIK3CA 突变相关。在 TCGA 验证队列中也观察到了类似的结果，该队列还显示了混合程度与通过 PyClone 估计的克隆群体数量之间的正相关。LumA-LumB 混淆占主导地位，但也存在其他组合。在两个队列中，混合程度均与总生存率相关，在 TCGA 中，混合程度与无病生存率相关，与年龄、分级和分期无关（HR=2.85，第三层与第一层相比）。
基于 PAM50 亚型纯度对 Luminal A 乳腺癌进行分组支持这样一种假设，即混合病例具有更差的临床特征和生存率。未来的分析将探索更广泛的基因组混合度量标准及其在单个肿瘤内的空间意义。
