Open Access Highly Accessed Open Badges Research

A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions

Alayne L Brunner1, Jun Li2, Xiangqian Guo1, Robert T Sweeney1, Sushama Varma1, Shirley X Zhu1, Rui Li1, Robert Tibshirani34 and Robert B West1*

Author Affiliations

1 Department of Pathology, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305-5324, USA

2 Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, 153 Hurley Hall, Notre Dame, IN 46556, USA

3 Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA 94305-4065, USA

4 Department of Health Research and Policy, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305-5405, USA

For all author emails, please log on.

Genome Biology 2014, 15:R71  doi:10.1186/gb-2014-15-5-r71

Published: 23 May 2014



The earliest recognizable stages of breast neoplasia are lesions that represent a heterogeneous collection of epithelial proliferations currently classified based on morphology. Their role in the development of breast cancer is not well understood but insight into the critical events at this early stage will improve efforts in breast cancer detection and prevention. These microscopic lesions are technically difficult to study so very little is known about their molecular alterations.


To characterize the transcriptional changes of early breast neoplasia, we sequenced 3′- end enriched RNAseq libraries from formalin-fixed paraffin-embedded tissue of early neoplasia samples and matched normal breast and carcinoma samples from 25 patients. We find that gene expression patterns within early neoplasias are distinct from both normal and breast cancer patterns and identify a pattern of pro-oncogenic changes, including elevated transcription of ERBB2, FOXA1, and GATA3 at this early stage. We validate these findings on a second independent gene expression profile data set generated by whole transcriptome sequencing. Measurements of protein expression by immunohistochemistry on an independent set of early neoplasias confirms that ER pathway regulators FOXA1 and GATA3, as well as ER itself, are consistently upregulated at this early stage. The early neoplasia samples also demonstrate coordinated changes in long non-coding RNA expression and microenvironment stromal gene expression patterns.


This study is the first examination of global gene expression in early breast neoplasia, and the genes identified here represent candidate participants in the earliest molecular events in the development of breast cancer.