Abstract P6-16-03: Intrinsic subtypes and MRI patterns in brain metastasis associated with breast cancer
Authors: Williams Nicole , Varadan Vinay , Vadodkar Aditi , Miskimen Kristy , Kim Stephanie , Vinayak Shaveta , Silverman Paula , Barnholtz-Sloan Jill , Sloan Andrew , Thompson Cheryl , Rogers Lisa , Gilmore Hannah , Harris Lyndsay 
Published: May 2015

Abstract
Background: Breast cancer is the 2nd most common cancer to metastasize to the brain. The development of brain metastasis (BM) is associated with a lower median survival compared with other locations of metastasis and carries with it high morbidity and reduced quality of life. There are limited treatment options and virtually no approved targeted therapies for this disease. We have previously reported specific pathways enriched in BM compared to primary tumors and now further this study to examine pathways by intrinsic subtype and location of and number of BM.
Methods: Archival FFPE material was obtained from BM using pathology records; clinical data, including MRI images, was retrieved from medical records and institutional tumor registry under an IRB protocol. Tumor DNA/RNA was extracted from 2 mm cores macrodissected from the FFPE tissue blocks using the Qiagen AllPrep DNA/RNA FFPE kit. Gene expression profiling was performed using Affymetrix Human Transcriptome Array 2.0 microarray on BM samples for which sufficient RNA was available. Gene-level expression quantification was derived after RMA normalization using the Affymetrix Transcriptome Analysis Console. PAM50 subtypes were assigned by clustering samples using median-subtracted PAM50 gene expression levels. Differential gene expression was estimated using the non-parametric Mann-Whitney test, followed by assessment of false discovery rate using the Banjamini-Hochberg FDR methodology. Pathway enrichment analysis was performed using the NCI Pathway Interaction Database.
Results: Gene expression profiling showed the following intrinsic subtype distribution among all BM: luminal A 32% (19/59), luminal B 31% (18/59), HER2 enriched 7% (4/59), and basal subtype 31% (18/59). At time of development of BM 64% (38/59) of patients presented with a single lesion compared to 36% (21/59) of patients who presented with multiple lesions (p=0.12). Thirty-nine percent (7/18) of patients with basal subtypes were observed to present with multiple BM compared to 61% (11/18) non-basal subtypes (p=0.25). In addition, 12% (13/59) of BM were found to be exclusively dural-based lesions. They appeared more frequently in the luminal subtypes [11/13 vs 2/13; p=0.06]. A total of 314 genes were differentially expressed (Wilcox pval &lt; 0.05; FDR &lt; 0.01) between the basal and luminal subtypes. As expected, we found that the FOXA transcription factor network was up-regulated in luminal when compared to the basal subtype, whereas the FOXM1 transcription factor network was up-regulated in the basals. We also found a total of 28 genes to be significantly differentially expressed (Wilcox pval &lt; 0.05; FDR &lt; 0.01) between the dural and non-dural BM. The beta1 integrin and syndecan-1 pathways were significantly enriched, along with angiogenesis and lymphatic endothelium pathways. Key genes in these pathways (COL1A1, COL1A2, COL3A1, CDH11, were found to be at least 2-fold up-regulated in the dural BM compared to non-dural BM.
Conclusion: Identifying pathways that are differentially expressed between intrinsic subtypes may help us develop new targeted therapies to provide more treatment options for breast cancer patients with brain metastasis.
Citation Format: Nicole Williams, Vinay Varadan, Aditi Vadodkar, Kristy Miskimen, Stephanie Kim, Shaveta Vinayak, Paula Silverman, Jill Barnholtz-Sloan, Andrew Sloan, Cheryl Thompson, Lisa Rogers, Hannah Gilmore, Lyndsay Harris. Intrinsic subtypes and MRI patterns in brain metastasis associated with breast cancer [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 P6-16-03.