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Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

While transcriptomics have enhanced our understanding for cancer, spatial transcriptomics enable the characterisation of cellular interactions. Here, the authors integrate single cell data with spatial information for HER2 + tumours and develop tools for the prediction of interactions between tumour-infiltrating cells.

Alma Andersson
Ludvig Larsson
Joakim Lundeberg
ResearchOpen Access14 Oct 2021
Nature Communications

Volume: 12, P: 1-14
Spatial transcriptomics reveals substantial heterogeneity in triple-negative breast cancer with potential clinical implications

Triple-negative breast cancer (TNBC) is a heterogenous disease with several molecular subtypes previously described. Here the authors perform a spatial transcriptomics analysis on a series of 92 patients, providing additional insights into the heterogeneity of TNBC, with implications for clinical outcomes and therapy.

Xiaoxiao Wang
David Venet
Christos Sotiriou
ResearchOpen Access26 Nov 2024
Nature Communications

Volume: 15, P: 1-22
High-definition spatial transcriptomics for in situ tissue profiling

A dense, spatially barcoded bead array captures RNA from histological tissue sections for spatially resolved gene expression analysis.

Sanja Vickovic
Gökcen Eraslan
Patrik L. Ståhl
Research09 Sept 2019
Nature Methods

Volume: 16, P: 987-990
Integrating spatial gene expression and breast tumour morphology via deep learning

Deep learning can predict spatial variations in gene expression from haematoxylin-and-eosin-stained histopathology images of patients with cancer.

Bryan He
Ludvig Bergenstråhle
James Zou
Research22 Jun 2020
Nature Biomedical Engineering

Volume: 4, P: 827-834
The spatial RNA integrity number assay for in situ evaluation of transcriptome quality

Kvastad et al. develop the spatial RNA Integrity Number (sRIN) assay that evaluates the RNA integrity at cellular resolution. This method improves the resolution of a similar method called the RNA Integrity Number (RIN), demonstrating spatial variation in the quality of RNA samples.

Linda Kvastad
Konstantin Carlberg
Joakim Lundeberg
ResearchOpen Access08 Jan 2021
Communications Biology

Volume: 4, P: 1-8

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Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

Spatial transcriptomics reveals substantial heterogeneity in triple-negative breast cancer with potential clinical implications

High-definition spatial transcriptomics for in situ tissue profiling

Integrating spatial gene expression and breast tumour morphology via deep learning

The spatial RNA integrity number assay for in situ evaluation of transcriptome quality

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