Abstract 785: Gene expression profiling identifies two stable clusters of lobular carcinoma in situ
Authors: Andrade Victor P. , Morrogh Mary , Dilip Giri , Qin Li-Xuan , Sakr Rita , Olvera Narciso , Paik Wooyul , Shirin Muhsen , Brodi Edi , Morrow Monica , King Tari A. 
Published: February 2011

Abstract
INTRODUCTION: Historical data suggests that lobular carcinoma in situ (LCIS) is not a precursor to invasive cancer but rather is a marker of increased risk, conferred equally to both breasts. Emerging evidence of genomic similarities between some LCIS and invasive cancers suggests that as subset of LCIS may exhibit precursor potential. The aim of this study was to look for evidence of distinct molecular subtypes of LCIS using cDNA microarray gene expression analysis.
METHODS: Mastectomy specimens from 9 patients with classical LCIS only, 74 patients with classical LCIS & synchronous invasive cancer (51 ILC, 16 IDC, 7 mixed) and 5 patients with LCIS + DCIS were selectively sampled using laser capture microdissection. Representative patient matched normal (NL), LCIS and invasive cells were microdissected from fresh frozen (FF) tissue samples. RNA was extracted and hybridized to Affy. HG-U133A 2.0 oligonucleotide arrays. Unsupervised hierarchical clustering of all LCIS samples and matched paired analysis of NL vs LCIS and LCIS vs ILC were performed using the R software (bioconductor package) and data were analyzed with Ingenuity Pathway Analysis filtered for human genes; p 2.
RESULTS: Suitable RNA was obtained from 48 FF LCIS samples. Patient matched NL and ILC samples were available for 42 and 17 cases, respectively. Hierarchical cluster analysis of all LCIS (n=48) demonstrated two stable clusters with median co-cluster frequency of 79% and 83%. The NL vs LCIS paired comparison (n=42) showed 306 differentially expressed genes (DEG) in Cluster 1 (FC &gt;2: 3.9% DEG) and 2012 DEG in Cluster 2 (FC &gt;2: 2.5% DEG). There were no common DEGs with FC &gt; 2 between clusters 1 and 2 for the NL vs LCIS comparison. The LCIS vs ILC paired comparison (n=17) showed 87 DEG in Cluster 1 (FC &gt;2: 58.6%) and 339 DEG in Cluster 2 (FC &gt;2: 27.7% DEG). There were 18/87 (21%) shared DEG between Cluster 1 and Cluster 2 for the LCIS vs ILC comparison. The functions of these 18 genes include biologically relevant genes involved in cell adhesion, cell-matrix interaction, cell movement, subcellular organization and cell proliferation.
CONCLUSION: Unsupervised hierarchical analysis demonstrated two stable distinct clusters of LCIS. Matched paired analysis of NL vs LCIS suggests that LCIS in cluster 1 is more similar to NL epithelium than LCIS in cluster 2. The absence of overlap in DEG with FC &gt; 2 for this comparison suggests that the initiation of lobular neoplasia may be driven by alternate genes in these two clusters. Matched paired analysis of LCIS vs ILC demonstrates 3.89 times more DEG in cluster 2 than 1, however the proportion of genes with FC &gt;2 was 2.2 times higher in cluster 1, suggesting both quantitative and qualitative differences in these groups. These preliminary analyses support the hypothesis that LCIS is a heterogeneous lesion, further analysis to determine if there is a subtype of LCIS with true precursor potential is underway.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 785.