Abstract 3027: Single-cell RNA sequencing defines regulatory networks in ER+ breast cancer organ-specific metastases
Authors: Just Nuria Padilla , Finlay-Schultz Jessica , Gillen Austin E. , Cittelly Diana M. , Wellberg Elizabeth A. , Horwitz Kathryn B. , Kabos Peter , Sartorius Carol A. 
Published: August 2018

Patients with estrogen receptor (ER)+ breast cancer are at chronic and prolonged risk of metastatic recurrences, which are usually fatal. The most frequent sites of ER+ breast cancer metastasis are bone, liver, lung, and brain, with individual tumors preferring one or more sites. The underlying mechanisms of site-specific metastasis are poorly understood and are critical for prevention and treatment of metastases to more lethal (brain, liver, lung) vs. static (bone) sites. The purpose of this study is to use single-cell RNA sequencing (sc RNA-seq) of ER+ breast cancer cells dispersed to breast tropic sites to define unique molecular determinants of organ-specific metastasis. Our group has developed ER+ patient-derived xenografts (PDX) at the University of Colorado Denver (UCD) labeled with constitutive luciferase-GFP. Our ER+ PDX fall into two general categories-pure “luminal” tumors with high ER plus/minus progesterone receptor (PR) (&gt;50% of cells) and an absence of cytokeratin 5 (CK5)+ cells, and “luminobasal” tumors with a low percent of ER+PR+ cells (5-10%) and high CK5+ cells (15-90%). Using intracardiac (ic) dispersal as a measure of late-stage metastasis, we have defined the organ homing preference of several of these lines. Luminal PDX frequently colonize bone, with occasional secondary lesions to brain and liver. Luminobasal PDX ubiquitously colonize liver, with secondary lesions mostly to lung. We performed sc RNA-seq of luminal UCD65 brain metastatic and luminobasal UCD46 liver metastatic cells compared to their cognate primary tumors grown in the mammary fat pad. UCD65 brain metastatic vs. primary tumor cells have elevated expression of PR and carbonic anhydrase 2 (CA2), a cellular guard against intracellular pH changes, and a prospective PR-regulated gene. UCD46 liver metastatic cells have activated TGFbeta signaling, and increased cancer stem cell markers. We conclude that ER+ breast cancer PDX retain innate preference for specific breast-tropic organs, that this may relate to their ER+ subtype (luminal vs. luminobasal), and that sc RNA-seq may identify key molecular signatures of ER+ breast cancer metastases. We are profiling additional tumors and sites to make further comparisons and generate testable hypotheses. Furthermore, our models allow for functional studies to test innovative interventions and therapeutics that target site-specific metastases.

This work was supported by grants from the Breast Cancer Research Foundation (16-072, CAS, KBH, PK), the NIH (CA140985, CAS) and the UCD RNA Biosciences Initiative (AEG, CAS, PK).

Citation Format: Nuria Padilla Just, Jessica Finlay-Schultz, Austin E. Gillen, Diana M. Cittelly, Elizabeth A. Wellberg, Kathryn B. Horwitz, Peter Kabos, Carol A. Sartorius. Single-cell RNA sequencing defines regulatory networks in ER+ breast cancer organ-specific metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3027.