DOI: 10.5281/zenodo.10638906
title: Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity

description: We acquired 10x Visium spatial transcriptomics (ST) data from 9 patients with invasive adenocarcinomas [1–5] to explore the role of the tumour microenvironment (TME) on intratumor heterogeneity (ITH) and drug response in breast cancer. By leveraging a new version of Beyondcell [6] (cnio-bu/beyondcell), a tool for identifying tumour cell subpopulations with distinct drug response patterns, we predicted sensitivity to over 1,200 drugs while accounting for the spatial context and interaction between the tumour and TME compartments. Moreover, we also used Beyondcell to compute spot-wise functional enrichment scores and identify niche-specific biological functions.

Here, you can find:

In signatures folder:



SSc breast: Collection of gene signatures used to predict sensitivity to > 1,200 drugs derived from breast cancer cell lines.

Functional signatures: Collection of gene signatures used to compute enrichment in different biological pathways.


In visium folder:



Visium objects: Processed ST Seurat objects with deconvoluted spots, SCTransform-normalised counts, and clonal composition predicted with SCEVAN [7]. These objects, together with the signatures, were used to compute the Beyondcell objects.


In single-cell folder:



Single-cell objects: Raw and filtered merged single-cell RNA-seq (scRNA-seq) Seurat objects with unnormalised counts used as a reference for spot deconvolution.


In beyondcell folder:



Beyondcell sensitivity objects with prediction scores for all drug response signatures in SSc breast.

Beyondcell functional objects with enrichment scores for all functional signatures.
description: The code used to create the SSc breast collection is available at cnio-bu/SSc-breast.

The data preprocessing pipeline that outputs the Seurat and Beyondcell objects is accessible at cnio-bu/ST-preprocess.

The code used to produce the final figures and tables is provided at cnio-bu/breast-bcspatial.
description: We downloaded luminal and TNBC 10x Visium ST data (CID4290, CID4535, 1142243F, 1160920F, CID4465 and CID44971) [1] from Zenodo (DOI: 10.5281/zenodo.4739739). HER2+ 10x Visium ST data (738811QB, 1168993F and V19L29), licensed under the Creative Commons Attribution licence, were downloaded from the 10x Genomics Datasets portal [4–5]. All these data included raw counts and matching tissue images. Wu et al. dataset also included metadata information with pathologist annotations for each spot. 10x Genomics provided an image with pathologist annotations for patient 738811QB, and we manually labelled each spot using Loupe Browser v5.0.1 [8]. Additionally, we downloaded scRNA-seq data [1] from the Single Cell Portal (ID: SCP1039) to construct the spot deconvolution reference.
description: References:

[1] Wu SZ, Al-Eryani G, Roden DL, Junankar S, Harvey K, Andersson A, et al. A single-cell and spatially resolved atlas of human breast cancers. Nat Genet. 2021;53:1334–47.

[2] 10x Genomics. Human Breast Cancer (Block A Section 1), Spatial Gene Expression Dataset by Space Ranger 1.1.0. 2020. Accessed 16 Jun 2023.

[3] 10x Genomics. Human Breast Cancer (Block A Section 2), Spatial Gene Expression Dataset by Space Ranger 1.1.0. 2020. Accessed 16 Jun 2023.

[4] 10x Genomics. Human Breast Cancer: Ductal Carcinoma In Situ, Invasive Carcinoma (FFPE), Spatial Gene Expression Dataset by Space Ranger 1.3.0. 2021. Accessed 16 Jun 2023.

[5] 10x Genomics. Human Breast Cancer: Visium Fresh Frozen, Whole Transcriptome, Spatial Gene Expression Dataset by Space Ranger 1.3.0. 2022. Accessed 16 Jun 2023.

[6] Fustero-Torre C, Jiménez-Santos MJ, García-Martín S, Carretero-Puche C, García-Jimeno L, Ivanchuk V, et al. Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data. Genome Med. 2021;13:187.

[7] De Falco A, Caruso F, Su X-D, Iavarone A, Ceccarelli M. A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data. Nat Commun. 2023;14:1074.

[8] 10x Genomics. Loupe Browser. Version 5.0.1. 2021.