Abstract S2-04: Comprehensive molecular characterization of invasive lobular breast tumors
Authors: Ciriello Giovanni , Gatza Michael L , Hoadley Katherine A , Zhang Hailei , Rhie Suhn K , Bowlby Reanne , Wilkerson Matthew D , Kandoth Cyriac , McLellan Michael , Cherniack Andrew , Laird Peter W , Sander Chris , King Tari A , Perou Charles M 
Published: May 2015

Abstract
Invasive lobular breast cancer (ILC) is the second most common histological subtype of breast cancer accounting for 10-15% of invasive breast tumors. ILC is typically ER+ and beyond the known mutation and/or loss of E-cadherin function, which contributes to a highly discohesive morphology, little is known about the additional mechanisms driving ILC tumorigenesis, or alterations that differentiate ILC from invasive ductal carcinomas (IDC).
Methods
A dataset of 817 breast tumors from the TCGA Project, including 490 IDC, 127 ILC and 88 samples with a mixed IDC-ILC histology, were profiled on six genomic platforms to develop a comprehensive atlas of mutational, epigenetic, transcriptional and proteomic data. Integrative genomic analyses, both supervised and unsupervised, of ILC tumors and across histological subtypes were performed to identify genomic drivers of ILC oncogenesis.
Results
Comprehensive multi-platform analyses identified distinct molecular events associated with ILC tumors. As expected, lack of E-cadherin protein, as determined by Reverse Phase Protein Array (RPPA), and CDH1 mRNA expression was uniformly observed in ILC cases associated with distinct alterations targeting CDH1. In addition to previously reported CDH1 and PIK3CA mutations, we identified a number of novel ILC-enriched recurrent mutations targeting PTEN, RUNX1, TBX3, and FOXA1.
An increased incidence of PTEN inactivating events, both mutations and copy number changes, were identified in ILC (13%) compared to IDC ER+ (7%), which corresponded with altered PTEN protein expression. These alterations were largely mutually exclusive with PIK3CA mutations and correlate with increased Akt activation as evident by increased Akt phosphorylation (pS473 and pT308), thus identifying a potential therapeutic opportunity for ILC patients.
GATA3 signaling, which regulates epithelial cell differentiation, is frequently altered in luminal/ER+ breast cancers. Our analyses determined GATA3 mutations are more frequent in IDC luminal tumors as compared to ILC (19 % vs 5%). ILC luminal tumors show significantly lower GATA3 protein expression, but a higher frequency of mutations in FOXA1 (9% vs 2% in Luminal IDC), a transcription factor required to promote ER transcriptional programs. Within ILC tumors, FOXA1 mutations were found to cluster into a specific region of the Forkhead (FK) DNA binding domain. A broader analysis of FOXA1 mutations in breast and prostate cancer confirm two specific hotspots in the FK domain and the C-terminal transactivation domain. Interestingly, these mutational classes are associated with distinct transcriptional changes suggesting different functional effects.
Finally, mRNA-seq analyses identified three robust molecular subclasses that are characterized by distinct genetic, genomic and proteomic patterns, including an increased immune-related group (Class 2), as well as differences in prognosis.
Conclusions
In this study, we developed a comprehensive atlas of genomic alterations that reveals key molecular differences differentiating ILC (FOXA1) from IDC (GATA3) tumorigenesis, a potential therapeutic target for ILC (Akt), and novel ILC subclasses based on underlying biological events. These findings provide further insight into the molecular heterogeneity of ER+ breast cancer.
Citation Format: Giovanni Ciriello, Michael L Gatza, Katherine A Hoadley, Hailei Zhang, Suhn K Rhie, Reanne Bowlby, Matthew D Wilkerson, Cyriac Kandoth, Michael McLellan, Andrew Cherniack, Peter W Laird, Chris Sander, Tari A King, Charles M Perou. Comprehensive molecular characterization of invasive lobular breast tumors [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr S2-04.