Oops, you're using an old version of your browser so some of the features on this page may not be displaying properly.

MINIMAL Requirements: Google Chrome 24+Mozilla Firefox 20+Internet Explorer 11Opera 15–18Apple Safari 7SeaMonkey 2.15-2.23

Poster discussion - Basic science

3520 - Single-cell RNA Sequencing of Triple Negative Breast Cancer Patient-Derived Xenograft Reveals Distinct Cellular Populations Spatially Mapped to Histological Sections


22 Oct 2018


Poster discussion - Basic science


Translational Research

Tumour Site

Breast Cancer


Constanza Martinez Ramirez


Annals of Oncology (2018) 29 (suppl_8): viii670-viii682. 10.1093/annonc/mdy304


C. Martinez Ramirez1, H. Kuasne2, M. Park2, D. Zuo2, C. Kleinman3, Y. Yang4, A. Blanchet-Cohen4, P. Savage5, J. Ragoussis6

Author affiliations

  • 1 Pathology, McGill University, H3A 1X1 - Montreal/CA
  • 2 Goodman Cancer Research Centre, McGill University, H3A 1X1 - Montreal/CA
  • 3 Lady Davis Research Institute, Jewish General Hospital, McGill University, H3A 0C7 - Montreal/CA
  • 4 Human Genetics, McGill University, H3A 0C7 - Montreal/CA
  • 5 Experimental Medicine, McGill University, H3A 1X1 - Montreal/CA
  • 6 Genome Québec Innovation Centre, McGill University, H3A 1A4 - Montreal/CA


Login to access the resources on OncologyPRO.

If you do not have an ESMO account, please create one for free.

Abstract 3520


Breast cancer is a heterogeneous disease consisting of distinct subtypes, including estrogen receptor positive, HER2 receptor positive and triple negative breast cancers (TNBC). The TNBC subtype lacks comprehensive targeted therapies and only 20-30% of patients have a complete response to neoadjuvant chemotherapy. TNBC present extensive genomic variation at the time of diagnosis and distinctive selective pressures exerted by treatment can promote the outgrowth of tumor subclones with the greatest survival characteristics. The overall aim of this project is to spatially map single-cell RNA-sequencing (scRNAseq) populations in primary and patient-derived xenograft (PDX) tumor sections, and further isolate and mechanistically study tumor subclones correlated with poor patient outcome.


We established a patient-derived xenograft (PDX) from a patient’s primary TNBC tumor. Single cells from the TNBC PDX tumor were obtained by enzymatic dissociation. Single-cell libraries were generated using the GemCode Single-Cell Instrument and Single Cell 3' Library & Gel Bead Kit v2 and Chip Kit (10x Genomics) according to the manufacturer’s protocol. The R package Seurat (v2.1) was used to analyze the single-cell RNA-seq data. Multiplex immunofluorescence (IF) was performed on primary and PDX tumors sections.


We identified seven different biological clusters as principal components in the scRNAseq analysis. For each cluster we selected specific genes that could exclusively represent each single population and exclude the others. We were able to successfully map all seven populations and identify a high correlation in the spatial cluster distribution between primary and PDX samples.


Using scRNAseq and multiplex IF we spatially superimposed single cell populations to human and PDX histological samples. This novel methodology represents a clinically relevant tool to spatially and temporally map specific cellular populations through disease progression and along treatment.

Clinical trial identification

Legal entity responsible for the study

Morag Park.


Stand Up To Cancer.

Editorial Acknowledgement


All authors have declared no conflicts of interest.

This site uses cookies. Some of these cookies are essential, while others help us improve your experience by providing insights into how the site is being used.

For more detailed information on the cookies we use, please check our Privacy Policy.

Customise settings
  • Necessary cookies enable core functionality. The website cannot function properly without these cookies, and you can only disable them by changing your browser preferences.