Microarray Data Analysis Using Peripheral Blood Samples Suggests Differential Enrichment of Signaling Pathways between Breast Cancer Patients and Normal Subjects.
Authors: Li X. , Hu H. , Shriver C. , Mural R. 
Published: December 2010

Abstract
Background: Breast cancer is the second most common cancer among women in the United States and the second leading cause of cancer death in women. Early and accurate diagnosis is crucial for better treatment and reduction of mortality. Diagnostics based on blood samples are being developed for many diseases including a variety of cancers.Gene expression profiling has been widely used to investigate the mechanisms of tumorigenesis with the goal of developing novel treatment strategies. We have applied microarray technology to study the gene expression signatures in blood samples from patients with invasive breast cancer, with benign breast disease and from disease free (normal) control groups to find potential diagnostic patterns. We have identified differentially expressed genes in each group and investigated the pathways these genes are involved in and how these are regulated.Material and Methods: Human blood samples from 102 invasive breast cancer patients, 57 patients with benign breast disease and 102 normal controls were collected for this study. Patients are enrolled in the Clinical Breast Care Project (CBCP) following HIPAA-compliant IRB approved protocols, with proven breast pathology diagnosis categories. Affymetrix HG-U133 Plus 2 GeneChips were used to investigate the gene expression profile. Microarray experiments were performed following Affymetrix protocols. CEL files were then analyzed with RMA algorithm for the calculation of gene expression matrix. Differentially expressed genes were identified between different groups using Wilcoxon rank sum test. We also applied Gene Set Enrichment Analysis (GSEA) to the entire gene expression profiles to investigate the gene sets or pathways enriched in different groups.Results: We identified about 2,051 differentially expressed genes between normal and invasive groups (p &lt; 0.001 and Fold Change &gt; 1.2). Furthermore, about 445 and 51 genes were identified in normal vs. benign and benign vs. invasive groups respectively. We performed GSEA using 395 gene sets from pathway databases, initially focusing on normal vs. invasive groups. 123 gene sets are highly expressed in the normal group and 272 gene sets are highly expressed in the invasive group. For the normal group, 10 gene sets are significantly enriched and 22 gene sets are significantly enriched in the invasive group (p &lt; 0.05). These results show that some important pathways are down regulated in the invasive group, such as, the B-cell antigen receptor pathway, the BCR signaling pathway, the T-cell signal transduction pathway, the IL4 receptor pathway, the PIP3 pathway, the ERK pathway, etc. The pathways up regulated in the invasive group are oxidative phosphorylation pathway, ATP synthesis, etc.Discussion: Our results suggest that a list of genes differentially expressed in different groups and they may be used to compose cancer marker panels which can be integrated with currently clinical procedures for cancer diagnosis. We also find some crucial pathways enriched in each group. Most of the pathways downregulated in the blood of patients in the invasive group are related to the immune response. In contrast, most of pathways upregulated in the blood of patients in the invasive group are associated with metabolism.
Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3024.