Genome-wide expression profiling of microdissected human breast tumor cells: tumor classification predictive of metastases and clinical outcome

We are analyzing human breast tumors and metastases with Affymetrix U133 Plus 2.0 GeneChips, following isolation of uniform tumor cell populations by laser-capture microdissection and linear amplification of RNA. Genome-wide expression profiles of currently 68 breast carcinomas, eight lymph node metastases, and eight normal breast samples were determined, and were correlated with detailed clinical outcome data to identify new and improved diagnostic marker genes of breast cancer. These marker genes were validated by real-time PCR as well as by IHC and/or FISH on tissue arrays. We identified a set of genes by which these patients could be classified into those with a short overall survival and those with a good prognosis with high accuracy (P < 0.0006). The prognostic markers thus identified included the estrogen receptor (ESR1), a known key prognostic marker gene of breast cancer. Defined sets of <60 genes each were identified that discriminated significantly (P < 0.01) between control patients and patients who develop lymph node, bone, or lung metastases, or other distant metastases. In contrast, >1000 genes were differentially expressed in primary tumors progressing to liver metastases, thus identifying a novel breast cancer subclass comprising ~15% of our cases. Downregulation of p14A and p14B, two homologous proteins of unknown function, was found to be associated with lung metastases. Tumors expressing high levels of p14A and p14B do not metastasize to the lung, tend to have a low tumor grade, are predominantly hormone receptor-positive, and are associated with a longer overall survival. This metastasis suppressor activity of p14A and p14B appears to be lung-specific, as no effect on liver metastasis and only a slight delay on bone metastasis formation were observed in tumors expressing high levels of p14A or p14B. We also identified ~75 genes coregulated with HER2, an RTK oncogene highly relevant to breast cancer therapy. Sixteen out of the 20 genes most closely co-expressed (P < 10^-5) are located in the same chromosomal region as HER2, suggesting that this entire region is co-amplified in ~20–30% of breast carcinomas. Furthermore, a potential key role in breast cancer progression of the PI3K/mTOR and the WNT signaling pathways was strongly suggested by our expression profiles. We found that stimulation of protein synthesis and cell growth via PI3K, mTOR, and eIF4E is the primary function of IGF signaling, and that activation of the WNT pathway in breast tumors significantly correlated with metastases and poor prognosis.