Abstract P2-06-01: Intrinsic transcriptomic differences of luminal progenitors and mature luminal cells of the normal breast
Authors: Fang Fang , Bhat-Nakshatri Poornima , Anjanappa Manjushree , Rusch Dough , Buechlein Aaron , Miller Dave , Nephew Kenneth P , Nakshatri Harikrishna 
Published: March 2020

Abstract
Epithelial cells in the normal breast are organized hierarchically into stem, luminal progenitor (LP) and mature luminal cells (LC) with distinct gene expression patterns. However, whether these gene expression differences are cell-intrinsic, driven through LP-LC cell interactions or due to stromal-luminal cell interactions in the breasts of healthy women is incompletely understood. Furthermore, prior studies on these cell populations did not take genetic ancestry into consideration despite widely reported genetic ancestry-dependent differences in the normal breast biology and breast cancer susceptibility/outcome. We isolated LP and LC breast epithelial cells from core breast biopsies of healthy women representing European, African American and Latino ancestry (five each). After a brief propagation (five passages) under epithelial reprogramming assay conditions, transcriptomes and DNA methylomes were examined using RNA- and Methylcapture-sequencing. Differences in gene expression (FDR&lt;0.05, fold change &gt;2) in LC cells compared to LP cells were observed, with 1581 and 609 genes up- and down-regulated, respectively. These data were enriched for signaling networks associated with cell cycle control of chromosomal replication, mitotic roles of polo-like kinase (down-regulated genes), granulocyte adhesion and diapedesis and LXR/RXR signaling (up-regulated genes). Despite marked gene expression differences between LC and LP cells, only 14 upregulated genes and four down-regulated genes showed DNA hypo- and hyper-methylation, respectively, in LC cells compared to LP cells, suggesting a minimal role for DNA methylation in differential gene expression between the two cell types. Furthermore, of the 2190 differentially expressed genes, 7% (158 genes) were regulated by estrogen, suggesting that differences in hormone responsiveness contribute to differential gene expression in LP and LC cells. To determine relationships between genes differentially methylated and expressed in LC and LP cells and breast cancer, we used publicly available databases, including TCGA. Interestingly, all genes hypermethylated and expressed at lower levels in LC cells were similarly hypermethylated and expressed at lower levels in breast cancers compared to normal breast, suggesting that these genes are minimally altered in breast cancer. Furthermore, in LC compared to LP cells, of thegenes hypomethylated and expressed at higher levels, only four genes (AIM1L, PRSS27, PTK6 and UNC13D) showed a similar pattern in breast tumors compared to normal breast. Of these, PTK6 is significantly overexpressed in luminal and HER2+ breast cancers compared to basal-like breast cancers, suggesting that PTK6+ cells are the preferred cell-of origin of luminal breast cancers. Taken together, this is the first study to demonstrate that transcriptomic data of normal breast cells from healthy women can be used to further define cell-of-origin of tumors and identify cancer-specific gene expression changes in breast cancer.
Citation Format: Fang Fang, Poornima Bhat-Nakshatri, Manjushree Anjanappa, Dough Rusch, Aaron Buechlein, Dave Miller, Kenneth P Nephew, Harikrishna Nakshatri. Intrinsic transcriptomic differences of luminal progenitors and mature luminal cells of the normal breast [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-06-01.