[Frontiers in Bioscience E3, 125-136, January 1, 2011]

BRCA1-related gene signature in breast cancer: the role of ER status and molecular type

Katarzyna Marta Lisowska1, Volha Dudaladava1,2, Michal Jarzab1, Tomasz Huzarski3, Ewa Chmielik4, Ewa Stobiecka4, Jan Lubinski3, Barbara Jarzab5

1Department of Tumor Biology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland, 2currently: Department of Medical Biology and Genetics, Grodno State Medical University, Grodno, Belarus, 3International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland, 4Department of Pathology Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland, 5Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Material and methods
3.1. Clinical samples
3.2. BRCA1 mutation-testing
3.3. RNA isolation
3.4. Detection of BRCA1 promoter methylation
3.5. Oligonucleotide micorarrays
3.6. Quantitative RT-PCR
3.7. Methods of data analysis
3.8. Data analysis workflow
4. Results
4.1. Search for the BRCA1-mutation signature in breast cancer
4.2. BRCA1-related expression signature is strongly influenced by ER status of the tumor
4.3. The biological context of the gene expression differences between BRCA1-mutated and sporadic tumors
4.4. BRCA1 expression signature in the context of differences between basal and luminal subtype of breast cancer
4.5. Q-PCR verifies whether changes in gene expression are related to the BRCA1 mutation status or to other factors
4.6. The impact of BRCA1 inactivation (mutation or methylation) on gene expression profile in breast cancer
4.7. Unsupervised analysis confirms that main sources of molecular variability are ER status and molecular subtype
5. Discussion
6. Acknowledgments
7. References

1. ABSTRACT

There is an ongoing debate whether hereditary breast cancer is a clinical entity distinct from sporadic breast cancer. We tried to shed some light on this issue by comparing the molecular profiles of these two types of cancer using DNA microarrays. Our results show that a previously reported marked difference between BRCA1-mutation linked and sporadic breast cancer was probably due to uneven stratification of samples with different ER status and basal-like versus luminal-like subtype. We observed that apparent difference between BRCA1-linked and other types of breast cancer found in univariate analysis was diminished when data were corrected for ER status and molecular subtype in multivariate analyses. In fact, the difference in gene expression pattern of BRCA1-mutated and sporadic cancer is very discrete. These conclusions were supported by the results of Q-PCR validation. We also found that BRCA1 promoter hypermethylation had similar effect on global gene expression as mutation-induced protein truncation. Thus, in the molecular studies of hereditary breast cancer, BRCA1 promoter methylation should be recognized and considered together with gene mutation.