Abstract P3-08-14: Quantifying intrinsic subtype admixture in luminal A breast cancer and its relationship to clinical outcomes
Authors: Kumar N , Zhao D , Sethi A , Gann PH 
Published: May 2019

Abstract
Background/Objectives: PAM50 gene profiling assigns each cancer to a single intrinsic subtype. However, individual cancers vary in their adherence to a prototype, and 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 cases according to their degree of subtype admixture, and then relate such admixture to clinical and molecular variables.
Methods: We re-constructed scaled, normalized PAM50 profiles for 1,980 cases (674 LumA) in the METABRIC cohort and for each case we computed its Mahalanobis (M-) distance from its assigned centroid and its M-distance from all other centroids. We used t-SNE plots to visualize overlaps in subtype clustering. With Normal-like cases excluded, Median Distance Criteria (MDC) classified a case as Pure if it was located within the 50th percentile of the LumA centroid and &gt;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; cases were grouped by DRC tertile. Pure and admixed LumA cases were compared on clinical, molecular and survival traits. TCGA LumA cases (n=509) were used for independent validation.
Results: Compared to admixed cases in METABRIC, pure ones by MDC had younger age at diagnosis, smaller tumor size, lower grade and lower stage. Comparisons of the highest (T3, most admixed) to lowest tertile (T1) for DRC revealed even stronger associations. Admixed cases, by both metrics, were more likely to show HER2 gain, high proliferation by AURKA expression, higher PAM50 Risk of Recurrence scores, more frequent TP53 mutation, and less frequent mutation of PIK3CA and CBFB. Similar results were observed in the TCGA validation cohort. LumA-LumB confusion was predominant, but other combinations with LumA 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. (See table for adjusted hazard ratios).
Conclusions: 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.
Multivariable hazard ratios for overall (OS) and disease-free survival (DFS) for Luminal A breast cancer, according to degree of subtype admixture. METABRIC and TCGA cohorts. Distance ratio tertile T1 (pure)T2T3 HRadj95% CIHRadj95% CIHRadj95% CIP trendMETABRIC - OS*1.00-1.200.91-1.591.421.07-1.88&lt;0.001TCGA - OS^1.00-1.340.69-2.621.901.02-3.540.04TCGA - DFS^1.00-1.140.48-2.742.851.39-5.850.002* Adjusted for age, tumor size, grade and stage; ^ adjusted for age, size and stage only
Citation Format: Kumar N, Zhao D, Sethi A, Gann PH. Quantifying intrinsic subtype admixture in luminal A breast cancer and its relationship to clinical outcomes [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-08-14.