Oncogenic and drug-resistant transcriptional programs– a joint analysis of single-cell and bulk Exome/RNA-seq in Metastatic Breast Cancer

Ofir Cohen ^1,2 Daniel Abravanel ¹ Michal Slyper ² Johanna Klughammer ² Judit Jane-Valbuena ² Karla Helvie ¹ Laura Dellostritto ¹ Sebastien Vigneau ¹ Jingyi Wu ¹ Julia Waldman ² Orr Ashenberg ² Matan Hofree ² Mike Cuoco ² Eric Winer ¹ Nancy Lin ¹ Asaf Rotem ¹ Orit Rozenblatt-Rosen ² Bruce Johnson ¹ Aviv Regev ² Nikhil Wagle ^1,2

¹Department of Medical Oncology, Dana-Farber Cancer Institute, Center for Cancer Precision Medicine, USA
²Cancer Program, Cell Circuits, Klarman Cell Observatory, Broad Institute of MIT and Harvard, USA

While recent studies have begun to elucidate the genomics of metastatic breast cancer (MBC), the transcriptional programs that drive the drug-resistant phenotype remain poorly understood.

We prospectively collected biopsies from MBC patients with detailed clinicopathologic features. We profiled 29 biopsies by single-cell RNA-seq, as well as dual bulk whole exome/transcriptome on 265 biopsies. We analyzed 100,470 single-cell transcriptomes and generated a comprehensive MBC atlas of the tumor and tumor-microenvironment (TME). To increase our power to associate programs with clinicopathologic characteristics, we performed a joint analysis of the single-cell and bulk RNA-Seq data. For example, we found significant differences in the TME of liver metastases compared to other sites with liver metastases depleted in activated B-cells and cytotoxic T-cells, consistent with immunosuppression in the hepatic space. Leveraging the dual exome/transcriptome profiles, we characterized mutation-specific oncogenic programs. For example, we characterized the oncogenic program associated with drug-resistant estrogen receptor mutation (ESR1-mut). Beyond activation of expected ER signaling genes, ESR1-mut also included specific Interferon-stimulated genes (IFI6, ISG15, IFIT1, STAT1), associated with tamoxifen resistance (PMID-15657362) and ECM-mediated regulation of apoptosis (PMID-17016442), and genes associated with cell-migration (SOX9, AGR2, TXNIP, and S100 genes). We similarly recovered mutation-specific oncogenic programs, including for RB1, TP53, GATA3, FOXA1, HER2, and FGFR - forming a compendium of in-vivo oncogenic signatures.

To the best of our knowledge, this is the first integration of single-cell and bulk Exome/RNA-seq data in MBC, resulting in a comprehensive single-cell-resolution transcriptional atlas, and a catalog of oncogenic programs and clinicopathologic association with implications for precision-oncology.