Spatially Resolved Molecular Investigation of Triple Negative Breast Cancer

Triple-negative breast cancer (TNBC) is an aggressive disease that accounts for 10-20% of all breast cancer cases diagnosed annually in the U.S.1. Despite its prevalence, TNBC remains resistant to conventional therapies, leading to a poor prognosis. The lack of therapeutic targets, as well as the complexity of the disease, make it critical to further investigate the underlying biology in order to improve diagnosis and therapeutic outcome. Spatial transcriptomics technology has helped address the limitations of traditional pathology examination, by combining the benefits of histology and massive throughput of RNA-seq. We investigated serial sections of TNBC2, using the 10x Genomics Visium Spatial Gene Expression Solution, to resolve its tumorigenic expression profile. This assay incorporates ~5000 molecularly barcoded, spatially encoded capture probes in spots over which tissue is placed, imaged, and permeabilized, capturing native mRNA in an unbiased fashion. Imaging and NGS data are processed together resulting in gene expression mapped to image position. We demonstrated spatial patterns of gene expression that agreed with annotations from pathological examination. This was then combined with immunohistochemical staining for tumor infiltrating lymphocytes, a hallmark of TNBC. By aggregating data from serial sections, we improved the delineation of gene expression patterns and demonstrate improved statistical power for cell-type identification. We combined these data with 3’ single-nucleus RNA-seq from the same sample, generating cell-type expression profiles that were used to annotate cell-types observed at a given position. Finally, we used an enrichment strategy to select for cancer-associated genes and show concordance with the full transcriptome assay, suggesting that a targeted sequencing approach can be used where a fixed gene panel is appropriate. Results from these efforts suggest that spatial gene expression profiling can provide a powerful complement to traditional histopathology, enabling both targeted panels and whole-transcriptome discovery of gene expression. This detailed view of the tumor microenvironment, as it varies across the tissue space, provides essential insight into disease understanding and the development of potential new therapeutic targets.

Learning Objectives:

1. Understand the value of the Visium Spatial Gene Expression Solution and how it works

2.Explore how 10x Genomics products work together to provide insight into biology at resolution and scale

3. Learn how 3rd party tools, in combination with the Visium spatial gene expression technology, capture the power of new methods and algorithm