Background: Invasive lobular carcinoma (ILC) of the breast has distinct histological and molecular variations compared to invasive ductal carcinoma (IDC), including absence of the adhesion protein E-cadherin. Recently, molecular subtypes within ILC have been described, with an analysis from The Cancer Genome Atlas (Ciriello et al) identifying three distinct groups within ILC based on gene expression—reactive-like, immune-related, and proliferative. In this study, we applied this 60-gene classifier to a locally advanced cohort of ILC and mixed ILC/IDC cases from patients screening for the I-SPY 2 neoadjuvant chemotherapy trial.

Methods: The I-SPY 2 TRIAL is open to women with more locally advanced, clinically/molecularly (as assessed by MammaPrint) high risk breast cancer.  HR+HER2- MammaPrint Low risk patients ineligible for I-SPY 2 randomization are invited to join a MP Low risk registry.  131 ILC and mixed ILC/IDC tumors from these cohorts (I-SPY 2: n=80; low risk registry: n=51) with pre-treatment Agilent microarrays were available for analysis. We used the Classification to Nearest Centroid technique to assign TCGA subtype to our cohort.  We assessed association between TCGA subtype, clinical covariates and response to therapy using a chi-square test.  We also evaluated the Euclidean distance between each sample and the three subtype centroids.  In an exploratory analysis, we used consensus clustering based on the 1000 most varying genes within the HR+HER2- I-SPY ILC cases to generate new unsupervised groupings, and assessed the concordance with the TCGA reactive-like, immune-related and proliferative subtype assignments.

Results: Of the 131 patients included, most (79%) were HR+HER2-, 11% were HR+HER2+, 2% were HR-HER2+ and 8% were HR-HER2- for a total of 10% HR-.  66 were pure ILC, while 65 were mixed ILC/IDC.   Upon applying the TCGA 60-gene classifier, the distribution of ILC subtypes was as follows: 33 (25%) were classified as reactive-like, 50 (38%) were immune-related, and 48 (37%) were proliferative. 64% of triple negative cases were reactive-like; while the HR+HER2- and HER2+ cases were more likely to be in the proliferative or immune-related subtype (p=0.037).  Among the 80 I-SPY 2 cases, the overall pathologic complete response rate was low (16%) but equivalent to the overall HR+HER2- I-SPY2 population (16%).  This did not differ across the groups defined by the TCGA ILC subtypes (p=0.79).

Interestingly, a subset of cases assigned as reactive-like and immune-related were of similar distance to the proliferative subtype centroid as patients assigned to the proliferative subtype.   When we used consensus clustering to identify new subsets within our locally advanced ILC cohort, our unsupervised groupings had only 32% concordance with the TCGA ILC subtype assignments.  

Conclusion: The low concordance between our consensus cluster groupings and the TCGA subtype groupings may reflect underlying differences within a locally advanced cohort of ILC cases, like I-SPY, that may not be captured in the 60-gene classifier developed from the overall lower stage TCGA cohort.  These findings suggest that considerable molecular heterogeneity exists in lobular cancers, which merits further investigation.

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