Immediate Gene Expression Changes After the First Course of Neoadjuvant Chemotherapy in Patients with Primary Breast Cancer Disease

Purpose: Our goal was to identify genes undergoing expressional changes shortly after the beginning of neoadjuvant chemotherapy for primary breast cancer. Experimental Design: The biopsies were taken from patients with primary breast cancer prior to any treatment and 24 hours after the beginning of the neoadjuvant chemotherapy. Expression analyses from matched pair samples representing 25 patients were carried out with Clontech filter arrays. A subcohort of those 25 paired samples were additionally analyzed with the Affymetrix GeneChip platform. All of the transcripts from both platforms were queried for expressional changes. Results: Performing hierarchical cluster analysis, we clustered pre- and posttreatment samples from individual patients more closely to each other than the samples taken from different patients. This reflects the rather low number of transcripts responding directly to the drugs used. Although transcriptional drug response occurring during therapy differed between individual patients, two genes (p21WAF1/CIP1 and MIC-1) were up-regulated in posttreatment samples. This could be validated by semiquantitative and real-time reverse transcription-PCR. Partial least- discriminant analysis based on approximately 25 genes independently identified by either Clontech or Affymetrix platforms could clearly discriminate pre- and posttreatment samples. However, correlation of certain gene expression levels as well as of differential patterns and clusters as determined by a different platform was not always satisfying. Conclusions: This study has demonstrated the potential of monitoring posttreatment changes in gene expression as a measure of the pharmacodynamics of drugs. As a clinical laboratory model, it can be useful to identify patients with sensitive and reactive tumors and to help for optimized choice for sequential therapy and obviously improve relapse- free and overall survival.

[1]  Christian A. Rees,et al.  Molecular portraits of human breast tumours , 2000, Nature.

[2]  B. Gusterson,et al.  High complete remission rates with primary neoadjuvant infusional chemotherapy for large early breast cancer. , 1995, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[3]  E. Brown,et al.  Global transcription profiling of estrogen activity: estrogen receptor alpha regulates gene expression in the kidney. , 2003, Endocrinology.

[4]  S. Glück.  The expanding role of epirubicin in the treatment of breast cancer. , 2002, Cancer control : journal of the Moffitt Cancer Center.

[5]  M Baum,et al.  Polychemotherapy for early breast cancer: An overview of the randomised trials , 1998 .

[6]  F. Tirone.  The gene PC3(TIS21/BTG2), prototype member of the PC3/BTG/TOB family: regulator in control of cell growth, differentiation, and DNA repair? , 2001, Journal of cellular physiology.

[7]  Klaus Pantel,et al.  Molecular signature associated with bone marrow micrometastasis in human breast cancer. , 2003, Cancer research.

[8]  Christine Solbach,et al.  Identification of high risk breast-cancer patients by gene expression profiling , 2002, The Lancet.

[9]  Petri Auvinen,et al.  Are data from different gene expression microarray platforms comparable? , 2004, Genomics.

[10]  Christian A. Rees,et al.  Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[11]  S. Martino,et al.  Estrogen receptor (ER) and progesterone receptor (PgR), by ligand‐binding assay compared with ER, PgR and pS2, by immuno‐histochemistry in predicting response to tamoxifen in metastatic breast cancer: A Southwest Oncology Group study , 2000, International journal of cancer.

[12]  Thomas D. Schmittgen,et al.  Quantitative reverse transcription-polymerase chain reaction to study mRNA decay: comparison of endpoint and real-time methods. , 2000, Analytical biochemistry.

[13]  M. Polymeropoulos,et al.  Gene expression profiling detects gene amplification and differentiates tumor types in breast cancer. , 2003, Cancer research.

[14]  T. Soussi,et al.  The human BTG2/TIS21/PC3 gene: genomic structure, transcriptional regulation and evaluation as a candidate tumor suppressor gene. , 2002, Gene.

[15]  T. Powles,et al.  A reduction in the requirements for mastectomy in a randomized trial of neoadjuvant chemoendocrine therapy in primary breast cancer. , 1998, Annals of oncology : official journal of the European Society for Medical Oncology.

[16]  Carsten Peterson,et al.  Expression profiling to predict outcome in breast cancer: the influence of sample selection , 2002, Breast Cancer Research.

[17]  Frederick E. Petry,et al.  Principles and Applications , 1997 .

[18]  C K Osborne,et al.  Estrogen receptor status by immunohistochemistry is superior to the ligand-binding assay for predicting response to adjuvant endocrine therapy in breast cancer. , 1999, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[19]  S. Steinberg,et al.  Neoadjuvant chemotherapy in the combined modality approach of locally advanced nonmetastatic breast cancer. , 1987, Cancer research.

[20]  D. Wickerham,et al.  Effect of preoperative chemotherapy on local-regional disease in women with operable breast cancer: findings from National Surgical Adjuvant Breast and Bowel Project B-18. , 1997, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[21]  A. Borowsky,et al.  An antisense oligodeoxynucleotide to p21(Waf1/Cip1) causes apoptosis in human breast cancer cells. , 2003, Molecular cancer therapeutics.

[22]  M. Gorospe,et al.  Functional role of p21 during the cellular response to stress. , 1999, Gene expression.

[23]  F. Tirone.  The gene PC3TIS21/BTG2, prototype member of the PC3/BTG/TOB family: Regulator in control of cell growth, differentiation, and DNA repair? , 2001 .

[24]  Mike Clarke,et al.  Polychemotherapy for early breast cancer: an overview of the randomised trials , 1998, The Lancet.

[25]  F. Bertucci,et al.  Gene expression profiling of primary breast carcinomas using arrays of candidate genes. , 2000, Human molecular genetics.

[26]  Ronald Eugene Shaffer,et al.  Multi‐ and Megavariate Data Analysis. Principles and Applications, I. Eriksson, E. Johansson, N. Kettaneh‐Wold and S. Wold, Umetrics Academy, Umeå, 2001, ISBN 91‐973730‐1‐X, 533pp. , 2002 .

[27]  G. Hortobagyi,et al.  Correlation between HER‐2 expression and response to neoadjuvant chemotherapy with 5‐fluorouracil, doxorubicin, and cyclophosphamide in patients with breast carcinoma , 2003, Cancer.

[28]  T. Lemarchand-Béraud,et al.  The predictive value of estrogen and progesterone receptors' concentrations on the clinical behavior of breast cancer in women °clinical correlation on 547 patients , 1986, Cancer.

[29]  R. Berger,et al.  Identification of BTG2, an antiproliferative p53–dependent component of the DNA damage cellular response pathway , 1996, Nature Genetics.

[30]  Allison Jones,et al.  cDNA microarray analysis of genes associated with ERBB2 (HER2/neu) overexpression in human mammary luminal epithelial cells , 2003, Oncogene.

[31]  M. Trudeau,et al.  Epirubicin in combination with the taxanes. , 2001, Seminars in oncology.

[32]  Van,et al.  A gene-expression signature as a predictor of survival in breast cancer. , 2002, The New England journal of medicine.

[33]  Yudong D. He,et al.  Gene expression profiling predicts clinical outcome of breast cancer , 2002, Nature.

[34]  J. Stec,et al.  Gene expression profiles obtained from fine-needle aspirations of breast cancer reliably identify routine prognostic markers and reveal large-scale molecular differences between estrogen-negative and estrogen-positive tumors. , 2003, Clinical cancer research : an official journal of the American Association for Cancer Research.

[35]  Rolf Ackermann,et al.  Identifying Superficial, Muscle-Invasive, and Metastasizing Transitional Cell Carcinoma of the Bladder , 2004, Clinical Cancer Research.

[36]  Samuel Granjeaud,et al.  Prognosis of Breast Cancer and Gene Expression Profiling Using DNA Arrays , 2002, Annals of the New York Academy of Sciences.

[37]  W. Kuo,et al.  Associations between gene expressions in breast cancer and patient survival , 2002, Human Genetics.

[38]  M. J. van de Vijver,et al.  Breast cancer response to neoadjuvant chemotherapy: predictive markers and relation with outcome , 2003, British Journal of Cancer.

[39]  C. Osborne,et al.  Biologic markers as predictors of clinical outcome from systemic therapy for primary operable breast cancer. , 1999, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[40]  M. Campiglio,et al.  Role of HER2 in wound-induced breast carcinoma proliferation , 2003, The Lancet.

[41]  D. Cameron,et al.  Primary systemic therapy for operable breast cancer--10-year survival data after chemotherapy and hormone therapy. , 1997, British Journal of Cancer.

[42]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Philip M. Long,et al.  Breast cancer classification and prognosis based on gene expression profiles from a population-based study , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[44]  J. Jager,et al.  The prognostic significance of steroid receptor activity in tumor tissues of patients with primary breast cancer. , 1997, American journal of clinical oncology.

[45]  D. Botstein,et al.  Microarrays in primary breast cancer--lessons from chemotherapy studies. , 2001, Endocrine-related cancer.

[46]  M. Dowsett,et al.  Coordinate expression of apoptosis-associated proteins in human breast cancer before and during chemotherapy. , 2002, Clinical cancer research : an official journal of the American Association for Cancer Research.

[47]  Margaret A. Nemeth,et al.  Multi- and Megavariate Data Analysis , 2003, Technometrics.

[48]  Annuska M Glas,et al.  Gene expression profiles of primary breast tumors maintained in distant metastases , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[49]  Carsten O. Peterson,et al.  Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. , 2001, Cancer research.

[50]  M. Polymeropoulos,et al.  Genes that co-cluster with estrogen receptor alpha in microarray analysis of breast biopsies , 2001, The Pharmacogenomics Journal.

[51]  Joseph Geradts,et al.  Differential gene expression patterns in HER2/neu-positive and -negative breast cancer cell lines and tissues. , 2002, The American journal of pathology.

[52]  C. Sotiriou,et al.  Gene expression profiles derived from fine needle aspiration correlate with response to systemic chemotherapy in breast cancer , 2002, Breast Cancer Research.

[53]  R. Tibshirani,et al.  Copyright © American Society for Investigative Pathology Short Communication Expression of Cytokeratins 17 and 5 Identifies a Group of Breast Carcinomas with Poor Clinical Outcome , 2022 .

[54]  Danh V. Nguyen,et al.  Multi-class cancer classification via partial least squares with gene expression profiles , 2002, Bioinform..

[55]  R. Tibshirani,et al.  Repeated observation of breast tumor subtypes in independent gene expression data sets , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Anna L. Brown,et al.  Effect of preoperative chemotherapy on the outcome of women with operable breast cancer. , 1998, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[57]  A. Borowsky,et al.  An Antisense Oligodeoxynucleotide to p21Waf1/Cip1 Causes Apoptosis in Human Breast Cancer Cells1 , 2003 .

[58]  T. Powles,et al.  Randomized trial of chemoendocrine therapy started before or after surgery for treatment of primary breast cancer. , 1995, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[59]  Erik Johansson,et al.  Megavariate analysis of hierarchical QSAR data , 2002, J. Comput. Aided Mol. Des..

[60]  R. Salunga,et al.  Gene expression profiles of human breast cancer progression , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[61]  M. Tenenhaus,et al.  Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach , 2003, Human Genetics.

[62]  M. Dowsett,et al.  Reduced apoptosis and proliferation and increased Bcl-2 in residual breast cancer following preoperative chemotherapy , 1998, Breast Cancer Research and Treatment.

[63]  E. Devilard,et al.  Gene expression profiles of poor-prognosis primary breast cancer correlate with survival. , 2002, Human molecular genetics.

[64]  Vladimir B Bajic,et al.  Classifying the estrogen receptor status of breast cancers by expression profiles reveals a poor prognosis subpopulation exhibiting high expression of the ERBB2 receptor. , 2003, Human molecular genetics.

[65]  L. Milas,et al.  Apoptosis in murine tumors treated with chemotherapy agents. , 1995, Anti-cancer drugs.

[66]  L Namba,et al.  The molecular biology of mammary intraepithelial neoplasia outgrowths , 2003, Breast Cancer Research.

[67]  G. Bonadonna,et al.  Primary chemotherapy in operable breast cancer: eight-year experience at the Milan Cancer Institute. , 1998, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[68]  M J O'Hare,et al.  Linking gene expression patterns to therapeutic groups in breast cancer. , 2000, Cancer research.

[69]  Syed Mohsin,et al.  Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer , 2003, The Lancet.

[70]  Tatjana Crnogorac-Jurcevic,et al.  Combination of microdissection and microarray analysis to identify gene expression changes between differentially located tumour cells in breast cancer , 2003, Oncogene.

[71]  R. Tibshirani,et al.  Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[72]  S. Baek,et al.  Dual function of nonsteroidal anti-inflammatory drugs (NSAIDs): inhibition of cyclooxygenase and induction of NSAID-activated gene. , 2002, The Journal of pharmacology and experimental therapeutics.

[73]  Daniel Birnbaum,et al.  Breast cancer revisited using DNA array‐based gene expression profiling , 2003, International journal of cancer.

[74]  M. West,et al.  Gene expression predictors of breast cancer outcomes , 2003, The Lancet.

[75]  Identifying pre-post chemotherapy differences in gene expression in breast tumours: a statistical method appropriate for this aim , 2002, British Journal of Cancer.

[76]  A. Wolff,et al.  Preoperative therapy in breast cancer: lessons from the treatment of locally advanced disease. , 2002, The oncologist.

[77]  L. Milas,et al.  Induction of apoptosis in murine tumors by cyclophosphamide , 2004, Cancer Chemotherapy and Pharmacology.

[78]  J. Stec,et al.  Global Gene Expression Changes During Neoadjuvant Chemotherapy for Human Breast Cancer , 2002, Cancer journal.

[79]  Partha S. Vasisht.  Computational Analysis of Microarray Data , 2003 .

[80]  R. Spang,et al.  Predicting the clinical status of human breast cancer by using gene expression profiles , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[81]  A. Wolff,et al.  Early operable breast cancer , 2000, Current treatment options in oncology.

[82]  C. Osborne,et al.  Progesterone receptor status significantly improves outcome prediction over estrogen receptor status alone for adjuvant endocrine therapy in two large breast cancer databases. , 2003, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[83]  T. Karn,et al.  Molecular classification of breast cancer patients by gene expression profiling * , 2001, The Journal of pathology.

[84]  T. Powles,et al.  Apoptosis and proliferation as predictors of chemotherapy response in patients with breast carcinoma , 2000, Cancer.

[85]  J. Zaunders,et al.  Macrophage inhibitory cytokine 1 reduces cell adhesion and induces apoptosis in prostate cancer cells. , 2003, Cancer research.

[86]  W. E. Orr,et al.  Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epithelium cell lines. , 2003, Molecular vision.