Journal Article
. 2007 May;108(2).
doi: 10.1007/s10549-007-9590-z.

Gene expression patterns in formalin-fixed, paraffin-embedded core biopsies predict docetaxel chemosensitivity in breast cancer patients

Jenny C Chang 1 Andreas Makris  M Carolina Gutierrez  Susan G Hilsenbeck  James R Hackett  Jennie Jeong  Mei-Lan Liu  Joffre Baker  Kim Clark-Langone  Frederick L Baehner  Krsytal Sexton  Syed Mohsin  Tara Gray  Laura Alvarez  Gary C Chamness  C Kent Osborne  Steven Shak  
Affiliations
  • PMID: 17468949
  •     41 citations

Abstract

Previously, we had identified gene expression patterns that predicted response to neoadjuvant docetaxel. Other studies have validated that a high Recurrence Score (RS) by the 21-gene RT-PCR assay is predictive of worse prognosis but better response to chemotherapy. We investigated whether tumor expression of these 21 genes and other candidate genes can predict response to docetaxel. Core biopsies from 97 patients were obtained before treatment with neoadjuvant docetaxel (4 cycles, 100 mg/m2 q3 weeks). Three 10-microm FFPE sections were submitted for quantitative RT-PCR assays of 192 genes that were selected from our previous work and the literature. Of the 97 patients, 81 (84%) had sufficient invasive cancer, 80 (82%) had sufficient RNA for QRTPCR assay, and 72 (74%) had clinical response data. Mean age was 48.5 years, and the median tumor size was 6 cm. Clinical complete responses (CR) were observed in 12 (17%), partial responses in 41 (57%), stable disease in 17 (24%), and progressive disease in 2 patients (3%). A significant relationship (P<0.05) between gene expression and CR was observed for 14 genes, including CYBA. CR was associated with lower expression of the ER gene group and higher expression of the proliferation gene group from the 21 gene assay. Of note, CR was more likely with a high RS (P=0.008). We have established molecular profiles of sensitivity to docetaxel. RT-PCR technology provides a potential platform for a predictive test of docetaxel chemosensitivity using small amounts of routinely processed material.

Recommendations from the EGAPP Working Group: can tumor gene expression profiling improve outcomes in patients with breast cancer?
Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group.
Genet Med, 2009 Jan 07; 11(1). PMID: 19125125    Free PMC article.
A single-tube quantitative assay for mRNA levels of hormonal and growth factor receptors in breast cancer specimens.
Ayuko A Iverson, Cheryl Gillett, +12 authors, Sheng-Yung P Chang.
J Mol Diagn, 2009 Feb 20; 11(2). PMID: 19225135    Free PMC article.
Sequential docetaxel as adjuvant chemotherapy for early breast cancer (TACT): an open-label, phase III, randomised controlled trial.
Paul Ellis, Peter Barrett-Lee, +22 authors, TACT Trialists.
Lancet, 2009 May 19; 373(9676). PMID: 19447249    Free PMC article.
Genomic predictors of outcome and treatment response in breast cancer.
Lara Dunn, Angela Demichele.
Mol Diagn Ther, 2009 Jun 23; 13(2). PMID: 19537843
Review.
Vascular endothelial growth factor C mRNA expression is a prognostic factor in epithelial ovarian cancer as detected by kinetic RT-PCR in formalin-fixed paraffin-embedded tissue.
Bruno V Sinn, Silvia Darb-Esfahani, +10 authors, Carsten Denkert.
Virchows Arch, 2009 Nov 17; 455(6). PMID: 19911196
Taxanes: optimizing adjuvant chemotherapy for early-stage breast cancer.
Philippe L Bedard, Angelo Di Leo, Martine J Piccart-Gebhart.
Nat Rev Clin Oncol, 2009 Dec 10; 7(1). PMID: 19997076
Review.
Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue.
Janine Antonov, Vlad Popovici, +9 authors, Rolf Jaggi.
BMC Cancer, 2010 Feb 11; 10. PMID: 20144231    Free PMC article.
Evidence for qualified quantitative mRNA analysis in formalin-fixed and paraffin-embedded colorectal carcinoma cells and tissue.
Xiaobo Lu, Tahar van der Straaten, Marco Tiller, Xiaoxia Li.
J Clin Lab Anal, 2011 May 14; 25(3). PMID: 21567463    Free PMC article.
Physician survey of the effect of the 21-gene recurrence score assay results on treatment recommendations for patients with lymph node-positive, estrogen receptor-positive breast cancer.
Ruth Oratz, Benjamin Kim, +4 authors, Michael Broder.
J Oncol Pract, 2011 Jul 07; 7(2). PMID: 21731516    Free PMC article.
Differentially expressed genes in window trials are influenced by the wound-healing process: lessons learned from a pilot study with anastrozole.
Mary Morrogh, Victor P Andrade, +7 authors, Tari A King.
J Surg Res, 2011 Jul 23; 176(1). PMID: 21777924    Free PMC article.
Protein expression, survival and docetaxel benefit in node-positive breast cancer treated with adjuvant chemotherapy in the FNCLCC-PACS 01 randomized trial.
Jocelyne Jacquemier, Jean-Marie Boher, +12 authors, François Bertucci.
Breast Cancer Res, 2011 Nov 03; 13(6). PMID: 22044691    Free PMC article.
Early developments in gene-expression profiling of breast tumors: potential for increasing black-white patient disparities in breast cancer outcomes?
Donna H Odierna, Aimee Afable-Munsuz, +5 authors, Ninez A Ponce.
Per Med, 2011 Dec 23; 8(6). PMID: 22190978    Free PMC article.
Molecular profiling for personalized cancer care.
Raheela Ashfaq.
Clin Exp Metastasis, 2012 Jun 09; 29(7). PMID: 22678423    Free PMC article.
The drug cocktail network.
Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao.
BMC Syst Biol, 2012 Oct 12; 6 Suppl 1. PMID: 23046711    Free PMC article.
Gene expression profiling for guiding adjuvant chemotherapy decisions in women with early breast cancer: an evidence-based and economic analysis.
Medical Advisory Secretariat.
Ont Health Technol Assess Ser, 2010 Jan 01; 10(23). PMID: 23074401    Free PMC article.
Pharmacogenetics in breast cancer: steps toward personalized medicine in breast cancer management.
Sarah Rofaiel, Esther N Muo, Shaker A Mousa.
Pharmgenomics Pers Med, 2010 Jan 01; 3. PMID: 23226048    Free PMC article.
Current approaches for neoadjuvant chemotherapy in breast cancer.
Roisin M Connolly, Vered Stearns.
Eur J Pharmacol, 2013 Apr 03; 717(1-3). PMID: 23545358    Free PMC article.
Review.
Biasogram: visualization of confounding technical bias in gene expression data.
Marcin Krzystanek, Zoltan Szallasi, Aron C Eklund.
PLoS One, 2013 Apr 25; 8(4). PMID: 23613961    Free PMC article.
Evaluating the 21-gene assay Recurrence Score® as a predictor of clinical response to 24 weeks of neoadjuvant exemestane in estrogen receptor-positive breast cancer.
Takayuki Ueno, Norikazu Masuda, +12 authors, Masakazu Toi.
Int J Clin Oncol, 2013 Oct 09; 19(4). PMID: 24101215
Molecular tests as prognostic factors in breast cancer.
Marc J van de Vijver.
Virchows Arch, 2014 Feb 04; 464(3). PMID: 24487789
Review.
Adaptive designs for clinical trials assessing biomarker-guided treatment strategies.
J Wason, A Marshall, +2 authors, N Stallard.
Br J Cancer, 2014 Mar 29; 110(8). PMID: 24667651    Free PMC article.
Multigene Assays for Classification, Prognosis, and Prediction in Breast Cancer: a Critical Review on the Background and Clinical Utility.
P Sinn, S Aulmann, +6 authors, A Schneeweiss.
Geburtshilfe Frauenheilkd, 2014 Apr 29; 73(9). PMID: 24771945    Free PMC article.
Diagnostic tests based on gene expression profile in breast cancer: from background to clinical use.
Laura Zanotti, Alberto Bottini, +2 authors, Maria Rosa Cappelletti.
Tumour Biol, 2014 Jul 23; 35(9). PMID: 25048969
Review.
Correlation Between E-cadherin Immunoexpression and Efficacy of First Line Platinum-Based Chemotherapy in Advanced High Grade Serous Ovarian Cancer.
Branka Petrić Miše, Vesna Dobrić Telesmanić, +3 authors, Eduard Vrdoljak.
Pathol Oncol Res, 2014 Aug 12; 21(2). PMID: 25108408
Genome-based risk prediction for early stage breast cancer.
Christina Adaniel, Komal Jhaveri, Adriana Heguy, Francisco J Esteva.
Oncologist, 2014 Sep 05; 19(10). PMID: 25187476    Free PMC article.
Review.
Markers for the identification of late breast cancer recurrence.
Ivana Sestak, Jack Cuzick.
Breast Cancer Res, 2015 Apr 08; 17. PMID: 25848913    Free PMC article.
Review.
The relationship between quantitative human epidermal growth factor receptor 2 gene expression by the 21-gene reverse transcriptase polymerase chain reaction assay and adjuvant trastuzumab benefit in Alliance N9831.
Edith A Perez, Frederick L Baehner, +11 authors, Karla V Ballman.
Breast Cancer Res, 2015 Oct 03; 17(1). PMID: 26429296    Free PMC article.
Assessment of the prognostic and predictive utility of the Breast Cancer Index (BCI): an NCIC CTG MA.14 study.
Dennis C Sgroi, Judy-Anne W Chapman, +10 authors, Michael Pollak.
Breast Cancer Res, 2016 Jan 06; 18(1). PMID: 26728744    Free PMC article.
Comparing Breast Cancer Multiparameter Tests in the OPTIMA Prelim Trial: No Test Is More Equal Than the Others.
John M S Bartlett, Jane Bayani, +18 authors, OPTIMA TMG.
J Natl Cancer Inst, 2016 May 01; 108(9). PMID: 27130929    Free PMC article.
Using the 21-gene assay from core needle biopsies to choose neoadjuvant therapy for breast cancer: A multicenter trial.
Harry D Bear, Wen Wan, +8 authors, Amy P Sing.
J Surg Oncol, 2017 Apr 14; 115(8). PMID: 28407247    Free PMC article.
The E2F4 prognostic signature predicts pathological response to neoadjuvant chemotherapy in breast cancer patients.
Kenneth M K Mark, Frederick S Varn, +2 authors, Chao Cheng.
BMC Cancer, 2017 May 04; 17(1). PMID: 28464832    Free PMC article.
Towards decision-making using individualized risk estimates for personalized medicine: A systematic review of genomic classifiers of solid tumors.
Daniel M Trifiletti, Vanessa N Sturz, Timothy N Showalter, Jennifer M Lobo.
PLoS One, 2017 May 10; 12(5). PMID: 28486497    Free PMC article.
Systematic Review.
Neoadjuvant Model as a Platform for Research in Breast Cancer and Novel Targets under Development in this Field.
Santiago Escrivá-de-Romaní, Miriam Arumí, Esther Zamora, Meritxell Bellet.
Breast Care (Basel), 2018 Oct 16; 13(4). PMID: 30319327    Free PMC article.
Review.
Decision of Adjuvant Systemic Treatment in HR+ HER2- Early Invasive Breast Cancer: Which Biomarkers Could Help?
Marie Alexandre, Aurélie Maran-Gonzalez, +6 authors, Séverine Guiu.
Cancer Manag Res, 2019 Dec 19; 11. PMID: 31849525    Free PMC article.
Review.
The Correlation of Magee EquationsTM and Oncotype DX® Recurrence Score From Core Needle Biopsy Tissues in Predicting Response to Neoadjuvant Chemotherapy in ER+ and HER2- Breast Cancer.
Atilla Soran, Kaori Tane, Efe Sezgin, Rohit Bhargava.
Eur J Breast Health, 2020 Apr 15; 16(2). PMID: 32285033    Free PMC article.
The Potential Use of Tumour-Based Prognostic and Predictive Tools in Older Women with Primary Breast Cancer: A Narrative Review.
Sophie Gordon-Craig, Ruth M Parks, Kwok-Leung Cheung.
Oncol Ther, 2020 Jul 24; 8(2). PMID: 32700048    Free PMC article.
Review.
Gene signature-based prediction of triple-negative breast cancer patient response to Neoadjuvant chemotherapy.
Yanding Zhao, Evelien Schaafsma, Chao Cheng.
Cancer Med, 2020 Jul 22; 9(17). PMID: 32692484    Free PMC article.
Molecular characterization of breast cancer needle core biopsy specimens by the 21-gene Breast Recurrence Score test.
Debbie M Jakubowski, Helen Bailey, +7 authors, Frederick L Baehner.
J Surg Oncol, 2020 Jun 05;. PMID: 32497318    Free PMC article.
Validation of the 21-gene test as a predictor of clinical response to neoadjuvant hormonal therapy for ER+, HER2-negative breast cancer: the TransNEOS study.
Hiroji Iwata, Norikazu Masuda, +19 authors, Yasuo Ohashi.
Breast Cancer Res Treat, 2018 Sep 23; 173(1). PMID: 30242578    Free PMC article.
Selection of neoadjuvant treatment based on the 21-GENE test results in luminal breast cancer.
Serafin Morales Murillo, Ariadna Gasol Cudos, +6 authors, Antonieta Salud Salvia.
Breast, 2021 Feb 19; 56. PMID: 33601299    Free PMC article.
Response to neoadjuvant chemotherapy and the 21-gene Breast Recurrence Score test in young women with estrogen receptor-positive early breast cancer.
Tal Sella, Shari I Gelber, +17 authors, Ann H Partridge.
Breast Cancer Res Treat, 2020 Nov 06; 186(1). PMID: 33150547