Transcriptomic changes in human breast cancer progression as determined by serial analysis of gene expression

Abstract

Introduction: Genomic and transcriptomic alterations affecting key cellular processes such us cell proliferation, differentiation and genomic stability are considered crucial for the development and progression of cancer. Most invasive breast carcinomas are known to derive from precursor in situ lesions. It is proposed that major global expression abnormalities occur in the transition from normal to premalignant stages and further progression to invasive stages. Serial analysis of gene expression (SAGE) was employed to generate a comprehensive global gene expression profile of the major changes occurring during breast cancer malignant evolution.

Methods: In the present study we combined various normal and tumor SAGE libraries available in the public domain with sets of breast cancer SAGE libraries recently generated and sequenced in our laboratory. A recently developed modified t test was used to detect the genes differentially expressed.

Results: We accumulated a total of approximately 1.7 million breast tissue-specific SAGE tags and monitored the behavior of more than 25,157 genes during early breast carcinogenesis. We detected 52 transcripts commonly deregulated across the board when comparing normal tissue with ductal carcinoma in situ, and 149 transcripts when comparing ductal carcinoma in situ with invasive ductal carcinoma (P < 0.01).

Conclusion: A major novelty of our study was the use of a statistical method that correctly accounts for the intra-SAGE and inter-SAGE library sources of variation. The most useful result of applying this modified t statistics beta binomial test is the identification of genes and gene families commonly deregulated across samples within each specific stage in the transition from normal to preinvasive and invasive stages of breast cancer development. Most of the gene expression abnormalities detected at the in situ stage were related to specific genes in charge of regulating the proper homeostasis between cell death and cell proliferation. The comparison of in situ lesions with fully invasive lesions, a much more heterogeneous group, clearly identified as the most importantly deregulated group of transcripts those encoding for various families of proteins in charge of extracellular matrix remodeling, invasion and cell motility functions.

Figure 1

Hierarchical clustering of the most commonly different expressed genes between normal breast tissue and ductal carcinoma in situ (DCIS) groups (P < 0.01). Color scale at bottom of picture is used to represent expression level: low expression is represented by green, and high expression is represented by red.

Figure 2

Hierarchical clustering of the most commonly differentially expressed genes between ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) groups (P < 0.01). Color scale at bottom of picture is used to represent expression level: low expression is represented by green, and high expression is represented by red.

Figure 3

Classification in functional categories of affected transcripts. (a) Differentially expressed between normal breast tissue and ductal carcinoma in situ (DCIS) (P < 0.01). (b) Transcripts differentially expressed between DCIS and invasive ductal carcinoma (IDC) (P < 0.01).

Figure 4

Hierarchical clustering of downregulated genes in invasive ductal carcinoma (IDC) (P < 0.05). Color scale at bottom of picture is used to represent expression level: low expression is represented by green, and high expression is represented by red. DCIS, ductal carcinoma in situ.

Figure 5

Schematic model portraying some of the most significant transcriptomic changes observed in breast cancer progression. DCIS, ductal carcinoma in situ; IDC, invasive ductal carcinoma.