Breast Cancer Research and Treatment

, Volume 103, Issue 2, pp 197–208 | Cite as

Predicting response to primary chemotherapy: gene expression profiling of paraffin-embedded core biopsy tissue

  • Lida Mina
  • Sharon E. Soule
  • Sunil Badve
  • Fredrick L. Baehner
  • Joffre Baker
  • Maureen Cronin
  • Drew Watson
  • Mei-Lan Liu
  • George W. SledgeJr
  • Steve Shak
  • Kathy D. Miller
Clinical trial



Primary chemotherapy provides an ideal opportunity to correlate gene expression with response to treatment. We used paraffin-embedded core biopsies from a completed phase II trial to identify genes that correlate with response to primary chemotherapy.

Patients and Methods

Patients with newly diagnosed stage II or III breast cancer were treated with sequential doxorubicin 75 mg/M2 q2 wks × 3 and docetaxel 40 mg/M2 weekly × 6; treatment order was randomly assigned. Pretreatment core biopsy samples were interrogated for genes that might correlate with pathologic complete response (pCR). In addition to the individual genes, the correlation of the Oncotype DX Recurrence Score with pCR was examined.


Of 70 patients enrolled in the parent trial, core biopsies samples with sufficient RNA for gene analyses were available from 45 patients; 9 (20%) had inflammatory breast cancer (IBC). Six (14%) patients achieved a pCR. Twenty-two of the 274 candidate genes assessed correlated with pCR (p < 0.05). Genes correlating with pCR could be grouped into three large clusters: angiogenesis-related genes, proliferation related genes, and invasion-related genes. Expression of estrogen receptor (ER)-related genes and Recurrence Score did not correlate with pCR. In an exploratory analysis we compared gene expression in IBC to non-inflammatory breast cancer; twenty-four (9%) of the genes were differentially expressed (p < 0.05), 5 were upregulated and 19 were downregulated in IBC.


Gene expression analysis on core biopsy samples is feasible and identifies candidate genes that correlate with pCR to primary chemotherapy. Gene expression in IBC differs significantly from noninflammatory breast cancer.


Angiogenesis Proliferation Invasion Inflammatory breast cancer 



Supported in part by American Cancer Society grant # CRTG-00-199-01-CCE (KDM), a Career Development Award from the American Society of Clinical Oncology (KDM), the Breast Cancer Research Foundation (KDM, GWS), the Walter Cancer Institute (GWS) and by unrestricted research grants from Aventis and Amgen.


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Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Lida Mina
    • 1
  • Sharon E. Soule
    • 2
  • Sunil Badve
    • 3
  • Fredrick L. Baehner
    • 4
  • Joffre Baker
    • 4
  • Maureen Cronin
    • 4
  • Drew Watson
    • 4
  • Mei-Lan Liu
    • 4
  • George W. SledgeJr
    • 2
  • Steve Shak
    • 4
  • Kathy D. Miller
    • 2
  1. 1.Department of MedicineIndiana UniversityIndianapolisUSA
  2. 2.Division of Hematology and OncologyIndiana UniversityIndianapolisUSA
  3. 3.Department of Anatomic PathologyIndiana UniversityIndianapolisUSA
  4. 4.Genomic Health Inc.Redwood CityUSA

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