Abstract 1218: Development of comprehensive molecular portraits of lobular breast cancer within the RATHER (Rational Therapy for Breast Cancer) Consortium

Background: The RATHER Consortium aims to identify novel kinase targets for therapy in poor-prognosis subtypes of breast cancer for which there are currently no targeted therapies available; namely invasive lobular carcinomas (ILC) which represent 10% of breast tumors.

The RATHER approach differs in two fundamental ways from the ongoing cancer genome re-sequencing efforts. Firstly, the major cancer genome re-sequencing efforts focus on DNA sequence analysis of the whole genome. In RATHER, we identify and validate novel kinases as therapy targets in a more comprehensive way by analyzing the DNA sequence and by applying state-of-the-art proteomics, copy number analysis and gene expression profiling technologies to identify activated/altered kinases. Secondly, RATHER also differs by focusing on the lobular subtype of breast cancer.

Methods: One hundred and fifty ILC samples (fresh frozen) with >5years follow-up were collected from two institutes (Cambridge, NKI). All samples were processed following one standard operating protocol to isolate RNA, DNA and protein of high quality. We used a five-pronged approach to identify and validate novel kinase targets for therapy in ILC breast cancer, namely i) direct re-sequencing of the kinome of 150 ILC breast tumors, ii) determination of abundance and activation status of kinases in these tumors by reverse phase protein lysate array (RPPA) technology, iii) determination of copy number aberration (CNA) in kinase genes by SNP arrays, iv) mRNA quantitation of both genome and kinome using DNA microarrays and v)RNAseq of a subset of ILC tumors.

Results: Data from these independent genome-scale technologies were integrated, yielding a priority list of potential kinase targets for therapy in ILC breast cancer. Deep sequencing of the kinome has revealed somatic mutations characteristic of ILC, which are currently being validated via mass spectrometry-based genotyping technology and their possible effects confirmed with gene expression, protein expression and phosphorylation changes. In addition, a subset of the ILC samples was assessed via RNA sequencing approach to confirm expression of particular mutants. Known gene mutations in ILC such as loss of CDH1 were confirmed; furthermore, a high frequency of PI3K pathway alterations (50%) was observed. Gene expression analysis of such a large set of ILC can reveal subsets of these breast cancers that significantly regulate alternate biological processes. Such biological subsets are currently being validated with clinical and follow-up data.

Conclusion: The RATHER project aims to deliver proof-of-concept for novel therapeutic interventions, together with companion molecular diagnostic assays for patient stratification, for up to 10% of breast cancer patients, where current treatment options are unsatisfactory.

Citation Format: Justine K. Peeters, Ian Majewski, Leanne de Koning, Yue Fan, Finbarr Tarrant, Darran O'Connor, Jeroen Heijmans, Mireille Snel, Tesa Severson, Astrid Bosma, Magali Michaut, Lorenza Mittempergher, Suet-Feung Chin, Thierry Dubois, William Gallagher, Carlos Caldas, Rene Bernards, Iris Simon, RATHER Consortium. Development of comprehensive molecular portraits of lobular breast cancer within the RATHER (Rational Therapy for Breast Cancer) Consortium. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1218. doi:10.1158/1538-7445.AM2013-1218