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JCO Early Release, published online ahead of print Sep 6 2005
Journal of Clinical Oncology, 10.1200/JCO.2005.02.0818

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Received March 30, 2005
Accepted July 6, 2005

Gene Expression Profiles in Paraffin-Embedded Core Biopsy Tissue Predict Response to Chemotherapy in Women With Locally Advanced Breast Cancer

Luca Gianni *, Milvia Zambetti , Kim Clark , Joffre Baker , Maureen Cronin , Jenny Wu , Gabriella Mariani , Jaime Rodriguez , Marialuisa Carcangiu , Drew Watson , Pinuccia Valagussa , Roman Rouzier , W. Fraser Symmans , Jeffrey S. Ross , Gabriel N. Hortobagyi , Lajos Pusztai , and Steven Shak

From the Istituto Nazionale Tumori, Milan, Italy; The University of Texas M.D. Anderson Cancer Center, Houston, TX: Genomic Health Inc, Redwood City, CA; and Millennium Pharmaceuticals Inc, Cambridge, MA.

* To whom correspondence should be addressed. E-mail: gianni{at}istitutotumori.mi.it

Purpose: We sought to identify gene expression markers that predict the likelihood of chemotherapy response. We also tested whether chemotherapy response is correlated with the 21 gene Recurrence Score assay that quantifies recurrence risk.

Methods: Patients with locally advanced breast cancer received neoadjuvant paclitaxel and doxorubicin. RNA was extracted from the pretreatment formalin-fixed paraffin-embedded core biopsies. The expression of 384 genes was quantified using reverse transcriptase polymerase chain reaction and correlated with pathologic complete response (pCR). The performance of genes predicting for pCR was tested in patients from an independent neoadjuvant study where gene expression was obtained using DNA microarrays.

Results: Of 89 assessable patients (mean age, 49.9 years; mean tumor size, 6.4 cm), 11 (12%) had a pCR. Eighty-six genes correlated with pCR (unadjusted P < .05); pCR was more likely with higher expression of proliferation-related genes and immune-related genes, and with lower expression of estrogen receptor (ER) -related genes. In 82 independent patients treated with neoadjuvant paclitaxel and doxorubicin, DNA microarray data were available for 79 of the 86 genes. In univariate analysis, 24 genes correlated with pCR with P < .05 (false discovery, four genes) and a 32 genes showed correlation with P < .1 (false discovery, eight genes). The Recurrence Score was positively associated with the likelihood of pCR (P = .005), suggesting that the patients who are at greatest recurrence risk are more likely to have chemotherapy benefit.

Conclusion: Quantitative expression of ER-related genes, proliferation genes, and immune-related genes are strong predictors of pCR in women with locally advanced breast cancer receiving neoadjuvant anthracyclines and paclitaxel.


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