287P - Perturbation and stability of PAM50 subtyping in population-based primary invasive breast cancer

Background

PAM50 gene expression subtypes represent a cornerstone in molecular classification of breast cancer and are included in risk prediction models to guide therapy. We aimed to illustrate the impact of included genes and biological processes on subtyping while considering a tumor’s underlying clinical subgroup defined by ER, PR and HER2 status.

Methods

We used a population-representative and clinically annotated primary breast tumor cohort of 6233 samples profiled by RNA sequencing and applied a perturbation strategy of excluding co-expressed genes (gene sets) from the PAM50 centroids followed by nearest centroid classification.

Results

We demonstrate how PAM50 nearest centroid classification depends on biological processes present across, but also within, ER/PR/HER2 subgroups and PAM50 subtypes themselves. Our analysis highlights several key aspects of PAM50 classification. Firstly, we observed a tight connection between a tumor’s nearest and second nearest PAM50 centroid. Additionally, we show that second-best subtype is associated with overall survival in ER-positive, HER2-negative, and node-negative disease. We also note that ERBB2 has little impact on PAM50 classification in HER2-positive disease regardless of ER-status, that the Basal subtype is highly stable in contrast to the Normal subtype, and that the LumB subtype classification is mainly reliant on expression of proliferation-related genes and low expression of keratin-associated genes.

Conclusions

Improved consciousness of the commonly used PAM50 subtyping scheme will aid in our understanding and interpretation of breast tumors that have seemingly conflicting PAM50 classification when compared to clinical biomarkers. Our study adds further support in challenging the common misconception that PAM50 subtypes are distinct classes by illustrating that PAM50 subtypes in tumors represent a continuum that may have clinical implications.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.

Funding

Swedish Cancer Society, Swedish Research Council, Fru Berta Kamprads research foundation.

Disclosure

All authors have declared no conflicts of interest.