COMPARISON OF THE GENE EXPRESSION PROFILES OF METAPLASTIC BREAST CANCER AND BASAL-LIKE BREAST CANCER. Mangesh A. Thorat 1 , Tanuja M Shet 2 , Akira Morimiya 1 , Roshni F Chinoy 2 , Rajendra A. Badwe 3 , Sunil Badve 1
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BREAST CANCER AND BASAL-LIKE BREAST CANCER
Mangesh A. Thorat 1, Tanuja M Shet 2, Akira Morimiya 1, Roshni F Chinoy 2, Rajendra A. Badwe 3, Sunil Badve 1
1Dept. of Pathology & Translational Genomics Core, IU School of Medicine, 2Dept. of Pathology, Tata Memorial Hospital, Mumbai, India, 3Dept. of Surgical Oncology, Tata Memorial Hospital, Mumbai, India
LIST OF SERVICES
Metaplastic cancers of the breast (MCBs) are a distinct subgroup of breast cancers. These are a heterogeneous group of tumours with mixed epithelial and sarcomatoid components, or mixed adenocarcinoma and squamous cell carcinoma components. (1) Many studies have reported aggressive clinical behavior of these tumours associated with poor survival. (1-4) Recently, few studies (5, 6) have proposed that MCBs belong to basal-like subtype of invasive ductal cancers (IDC). High-throughput gene expression profiling followed by hierarchical clustering led to identification of breast cancer subtypes. (7) Such approach can reliably determine whether MCBs belong to basal-like breast cancers (BBCs). However, rarity of these tumors has been a handicap for conventional gene expression profiling. (8) If MCBs belong to basal-like subtype, these should cluster together on multi-parameter hierarchical clustering as in microarray. Number of parameters to be used for such clustering should be more than 100; (9) smaller number of markers (5, 6) can yield spurious results. We tested this hypothesis by performing quantitative gene expression analysis of 502 cancer-related genes on archived FFPE tumors using a novel cDNA-mediated annealing, selection, extension, and ligation (DASL) assay to identify clustering pattern and differentially expressed genes between MCBs and BBCs identified by their triple negative receptor status.
Gene expression profiling:Whole genomeFocused (DASL on FFPE), standard panel or customizedDASL Whole genome
Genotyping: Standard panel or customized, up to 1536 SNPs
miRNA expression profiling
Nucleic Acid quantitation using NanoDrop
RNA QC using Bioanalyzer
Additional details available at: http://www.cancer.iu.edu/research/facilities/translational_genomics/
Figure 1: A) Metaplastic breast cancer with squamous differentiation. (200X) B) Basal (triple negative) breast cancer. (400X)
Table 1: Patient Characteristics
Table 2: Genes under-expressed in squamous MCBs
QUALITY CONTROL AND ASSURANCES
We selected 8 MCBs with squamous differentiation (Figure 1A), and 25 IDCs, 11 of which were triple negative tumors (TN) (Figure 1B); clinical characteristics of these patients are described in Table 1. RNA (200 ng) was extracted using HighPure RNA Paraffin Kit (Roche Applied Bioscience, Indianapolis, IN, USA). RNA was pre-qualified using iScript (Bio-Rad Laboratories Inc, Hercules, CA, USA) to reverse transcribe and SYBR Green Master Mix (Applied Biosystems, Foster City, CA, USA) to perform qPCR. DASL assay was performed using the Sentrix Universal Array (Illumina Corp., San Diego, CA, USA) of 502 known cancer genes. Statistical analyses and clustering were performed using BeadStudio v3.0 (Illumina Corp.).
Unsupervised hierarchical clustering of 33 cases showed two main branches, MCB and IDC (Figure 2). IDC group broadly comprised two subgroups; 9-case-subgroup clustering farthest from MCB branch contained 7 TN (78%), and 16-case-subgroup between these branches contained 4 TN (25%). Analysis of TN (n=11) vs. MCBs (n=8) revealed significant down-regulation of 10 genes (after correction for false-discovery) in MCBs (Table 2). Number of differentially expressed genes without correction for false-discovery was 53.
Translational Genomics Core
635 Barnhill Drive, Indianapolis, IN 46202
Email: [email protected]
Dr. Sunil Badve (Core Director)
350 W 11th st., Indianapolis, IN 46202
Email: [email protected]
Figure 2: Unsupervised Hierarchical clustering
MCBs and TN have distinct gene expression profiles and do not cluster together as one group. Contrary to recent hypothesis, MCBs are a distinct group of breast cancers and do not belong to BBCs.