Abstract No. 
2022 San Antonio Breast Cancer Symposium
8-11 Dec

Association of MRI morphologic phenotype from unsupervised learning with breast cancer subtypes and treatment response

Li W, Le NN, Onishi N, Newitt DC, Gibbs JE, Wilmes LJ, Gennatas E, LeStage B, Esserman LJ, Hylton NM

Background: Breast cancer is a heterogeneous disease and can be categorized into clinically or biologically meaningful subtypes. Predictive models built by MRI biomarkers performed better when they are optimized by breast cancer subtype than models optimized in the full cohort [1]. Functional tumor volume (FTV) measured from breast MRI has been used to assess tumor response to neoadjuvant therapy longitudinally in the I-SPY 2 TRIAL. Tumors show distinct morphological patterns, or phenotypes, on MRI. Previous studies demonstrated that either qualitative or quantitative measurements characterizing these phenotypes may provide additional information about treatment response [2,3]. In this study, we investigated if MRI morphologic phenotypes defined by unsupervised clustering is associated with breast cancer subtype and pathologic complete response (pCR) after neoadjuvant chemotherapy (NAC).

Methods: A cohort of 990 patients enrolled in the I-SPY 2 TRIAL were included in this retrospective analysis. Patients were randomized to one of nine experimental drug arms or standard NAC, and pCR was assessed at surgery. DCE-MRI data acquired at pretreatment (T0) and early treatment (T1) were analyzed. Four subtypes of breast cancer were defined by immunohistochemistry (IHC) based on hormone receptor (HR) and HER2 status.

Radiomic features were extracted by PyRadiomics [4] using FTV masks from DCE-MRI. MRI morphologic phenotypes were determined based on unsupervised hierarchical clustering approach on extracted radiomic shape features plus FTV using Pearson correlation with agglomerative ward linkage. The associations between the unsupervised clusters of radiomic features and FTV with four IHC subtypes and pCR were evaluated using χ2 test of independence. Cramer’s V [5] were computed to measure the strength of association (higher Cramer’s V means stronger association). P-value < 0.05 was considered statistically significant.

Results: Three clusters were generated by unsupervised hierarchical clustering in a population of 910 patients included in our analysis (80 patients excluded due to missing pCR or DCE-MRIs). At T0, the unsupervised clusters showed statistically significant but weak association with pCR (Cramer’s V = 0.088, p = 0.029), but the association between the clusters and HR/HER2 subtypes did not reach significance (Cramer’s V = 0.055, p = 0.48). The unsupervised clusters based on T1 shape radiomic features showed statistically significant association with both pCR and HR/HER2 subtypes (p < 0.001 for both) with Cramer’s V of 0.231 and 0.154, respectively. Our results showed stronger association between pCR and cancer subtypes with MRI shape radiomic features at T1 than at T0.

Various pCR rates were observed in MRI clusters at T1. They were 56%, 36%, and 23% in Cluster 1, 2, 3, respectively. Table 1 shows pCR rates by HR/HER2 subtype in each cluster. In all sub-cohorts, pCR rate was highest in Cluster 1 and lowest in Cluster 3. In HR+/HER2-, the pCR rate in Cluster 1 was 2-fold of the pCR rates in Clusters 2 and 3-fold of Cluster 3. pCR rate was statistically significantly different depending on the MRI clusters in the sub-cohorts except for the HR/HER2+ sub-cohort: HR+/HER2-, p< 0.001; HR+/HER2+, p=0.021; HR-/HER2+, p=0.083; HR-/HER2-, p< 0.001.

Conclusion: MRI phenotype generated by unsupervised clustering using radiomic shape features at both pretreatment and early-treatment time points was associated with pCR outcome. Stronger association was observed at early-treatment time point. The association differed by subtype, with the strongest observed in HR+/HER2- and triple negative subtypes. Our results suggest that radiomic shape features derived from DCE-MRI may be helpful for early prediction of tumor response to NAC.


1. npj Breast Cancer 6, (2020).

2. Tomography 6, (2020).

3. Annals of Surgical Oncology 20, 3823–3830 (2013).

4. Cancer Research 77, e104–e107 (2017).

5. Korean Stat Soc 42, 323–328 (2013).

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