Abstract 2696: Spatially resolved whole transcriptome molecular investigation of FFPE triple positive breast cancer tumors using the Visium platform
Authors: Williams Stephen R. , Turkekul Mesruh , Jurek Aleksandra , Mignardi Marco , Mielinis Paulius , Weisenfeld Neil I. , Stoeckius Marlon , Chell James 
Published: July 2021

Abstract
Triple-positive breast cancer (TPBC) is a rare but aggressive form of human epidermal growth factor receptor 2 (HER2) positive cancer. It accounts for fewer than 10% of all new breast cancer diagnoses in the USA annually. TPBC routinely exhibits elevated levels of HER2, along with oncogenic cell surface estrogen receptors (ER) and progesterone receptors (PR), but the underlying phenotype and survival rates vary. To better understand TPBC heterogeneity, we examined the tumor microenvironment by characterizing the spatial distribution of cellular transcriptomes.
Spatial transcriptomics technology combines the benefits of histological techniques with the massive throughput and discovery power of RNA sequencing, addressing the limitations of traditional pathological examination. However, standard clinical workflows collect formalin-fixed paraffin-embedded (FFPE) tissue, which can significantly damage molecules such as RNA, making investigation of the underlying biology at the transcriptomic level intractable.
We utilized the 10x Genomics Visium Spatial Gene Expression Solution for FFPE tissue to analyze and resolve tumorigenic profiles of serial sections of TPBC samples. This assay incorporates ~5,000 barcoded, spatially encoded capture probes in spots on a slide onto which tissue is placed, imaged, and permeabilized. Native RNA is detected and quantified using an FFPE compatible whole transcriptome probeset. Imaging and sequencing data are processed, resulting in a spatially resolved transcriptional readout.
Expression profiles and spatially mapped clustering data from FFPE sections processed using the whole transcriptome probeset highly correlated with data from fresh-frozen tissue. The expression signatures also aligned with pathologist annotations combined with immunofluorescent staining to demarcate the tumor, stromal, and immune compartments as well as HER2, PR, and ER. These data were paired with single nucleus RNA-seq (Chromium Single Cell 3' assay), generating cell type expression profiles giving insight into cell-type co-localization.
Taken together, these results demonstrate that whole transcriptome profiling of FFPE tissues using the Visium platform provide a powerful complement to traditional histopathological methods. This technology allows analysis of the whole transcriptome across tissue sections with high sensitivity and specificity, paired with morphological context and protein co-detection. The pairing of the whole transcriptome profile of TPBC FFPE samples at both the single nucleus and spatial level provides a comprehensive understanding of the tumor architecture. This in-depth knowledge, enabled by Visium for FFPE tissues, can provide unprecedented insights into tumor biology, disease progression, predictive biomarkers, drug response and resistance, and development of therapeutic targets.
Citation Format: Stephen R. Williams, Mesruh Turkekul, Aleksandra Jurek, Marco Mignardi, Paulius Mielinis, Neil I. Weisenfeld, Marlon Stoeckius, James Chell. Spatially resolved whole transcriptome molecular investigation of FFPE triple positive breast cancer tumors using the Visium platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2696.