High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue

Overview

This dataset is associated with the article "High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis" published in Nature Communications. See the publication for full details on methods and results.

How to view data

Interactively explore data with our Xenium Explorer web demo for Sample #1, or with Xenium Explorer, by downloading a Xenium Output Bundle below. Load the Gene Groups CSV to create gene groups based on cell type markers. Follow these instructions to view the post-Xenium image or image alignment file in Xenium Explorer

Xenium In Situ

The Xenium In Situ platform uses a microscopy based read-out. A 5 μm FFPE tissue section was sectioned onto a Xenium slide and placed in the Xenium Analyzer instrument for multiple cycles of imaging. Each gene has a unique optical signature, facilitating decoding of the target gene, from which a spatial transcriptomic map was constructed across the entire tissue section. The Xenium data was registered with post-Xenium IF / H&E images (workflow is non-destructive to the tissue) and integrated with Chromium and Visium data.

Channel descriptions for IF staining:

• Channel 1 = 1:200 CD20, Goat anti-Mouse IgG-488 , (Abcam, Cat. No. ab219329, Thermo Fisher Cat. No. A-11029)
• Channel 2 = 1:1500 HER2, Goat anti-Rabbit IgG-594, (Abcam Cat. No. ab134182, Abcam Cat. No. ab150088)
• Channel 3 = DAPI (Thermo Fisher, Cat. No. 62248)

Biomaterials

Two formalin-fixed & paraffin-embedded (FFPE) breast cancer tissue blocks were obtained from Discovery Life Sciences. Sample #1 was annotated by a pathologist to be T2N1M0, Stage II-B, ER+/HER2+/PR−. Sample #2 was characterized as stage pT2 pN1a pMX, ER−/HER2+/PR−. Corresponding dissociated tumor cells for Sample #1, fresh frozen (FF) in liquid nitrogen, were also sampled from the same 2.5 cm biopsy. For the Chromium Flex workflow, two 25 μm curls were pooled as a single replicate. 5 μm sections from Sample #1 were taken from the FFPE tissue using a microtome. Two replicate 5 μm sections were taken each for Visium CytAssist and Xenium. A 5 μm section was also taken from Sample #2 for Xenium.

Pathology

The tissue block for Sample #1 has two Ductal Carcinoma In Situ (DCIS) regions of interest. DCIS1 had invasive carcinoma lesions scattered throughout the stromal connective tissue, surrounding a large aggregate of highly proliferative ductal carcinoma in situ with two central comedo necrotic formations. DCIS2 had a smaller round intermediate nuclear grade ductal hyperplasia of solid type with cells that showed mild to moderate variability in size, shape, and placement; variable coarse chromatin; and variably prominent nuclei. The tissue block for Sample #2 has normal duct regions as well as DCIS and invasive carcinoma lesions.

Cell Type Annotations

An excel spreadsheet with cell type annotations for Xenium, Visium, and Chromium Flex is available for download here. For Xenium Sample #1, both supervised (with cell type labels transferred from Flex data) and unsupervised annotations are provided.