Finding alternative splicing variants in breast cancer
Growing evidence indicates that alternative or aberrant pre-mRNA splicing takes place during the development, progression, and metastasis of breast cancer. However, what splicing changes are really important in tumorigenesis and cancer biology remains to be elucidated.

We used microarrays of junction oligonucleotides representing 120 alternative exons of 64 genes to detect splicing differences between breast cancer cells and normal human mammary epithelial cells. Several splicing alterations in genes including CD44, FAS, APLP2 and MYL6 were detected by microarrays and RT-PCR.

We also compared two breast cancer cell lines MCF7 (estrogen receptor positive) and MDA-MB-231 (estrogen receptor negative) cultured in two-dimensional (2D) flat dish or in three-dimensional (3D) Matrigel. Interestingly, only a subset of the splicing alterations between MCF7 and MDA-MB-231 cells detected in 2D samples was retained in 3D samples, suggesting culturing conditions affect splicing variations. We further compared splicing in MCF7 cells grown in dish, Matrigel, or xenograft in mouse and found at least one example that splicing variants expressed in xenograft could be identified in 3D but not in 2D cultures. Thus, our preliminary investigation indicates that microarrays can be used to identify splicing variants that potentially can be used as breast cancer markers.