Genetic markers of response to neoadjuvent therapy: Array-based gene expression profiling from serial core biopsies

E. C. Wooten, Jenny C. Chang, S. G. Hilsenbeck, S. Moshin, P. O'Connell

Research output: Contribution to journalArticlepeer-review


Adjuvant chemotherapy in patients with breast cancer reduces the risk of recurrence and death. Docetaxel (Taxotere) has one of the highest response rates as a single agent in breast cancer therapy, and is being evaluated in large, randomized phase III studies as adjuvant therapy. Preliminary results from these studies indicate that only a subset of women benefit from the addition of docetaxel. Selection of patients who would benefit from adjuvant docetaxel is one of the most important questions in the management of breast cancer today. Array technology now allows for the expression levels of thousands of genes to be examined simultaneously and compared to the relative sensitivity or insensitivity of the tumor to treatment. Therefore, we hypothesize that patterns of gene expression exist that can be used to distinguish breast cancers that would be susceptible or resistant to particular therapies. This study employs core biopsies from 35 women obtained prior to treatment with docetaxel. Clinical response is determined after 12 weeks of therapy. Total RNA is isolated from the core biopsies and doubled stranded complementary DNA is synthesized using an oligo dT primer containing a T7 RNA polymerase promoter. Labeling and linear amplification of 250-300 fold is achieved by in vitro transcription in the presence of biotylated ribonucleotides. The labeled cRNA is hybridized onto Affymetrix U95-A chips to determine expression patterns. To date, we have analyzed 21 samples. The majority of the samples hybridized have produced analyzable data. The amounts of total RNA and T7 tagged double stranded complementary RNA from the core biopsy varied from sample to sample. Concentrations below 2.5μg of total RNA or 8μg of amplified cRNA failed to consistently produce suitable hybridization signals. The gene expression levels from analyzable samples will be normalized and compared statistically to identify differentially expressed genes in responders and non-responders. Quantitative RT-PCR and immunohistochemistry will confirm differential gene patterns of expression. Identification of such genes for use as a simple predictive test for docetaxel sensitivity would permit selection of appropriate therapy for women who would benefit from this treatment, and reduce unnecessary treatment, toxicity and cost to all women with breast cancer.

Original languageEnglish (US)
Number of pages1
JournalBreast Cancer Research and Treatment
Issue number3
StatePublished - Jan 1 2001

ASJC Scopus subject areas

  • Oncology
  • Cancer Research


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