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Spatial and temporal dynamics of cancer-associated fibroblast niches in breast cancer

Pantaleo, Jessica LU orcid ; Sjölund, Jonas LU orcid ; Bolivar, Paulina LU ; Bocci, Matteo LU orcid ; Phung, Bengt LU ; Malmberg, Maria LU ; Jönsson, Göran B LU and Pietras, Kristian LU orcid (2026) In Breast cancer research : BCR 28.
Abstract
Background: Cancer-associated fibroblasts (CAFs) are the main constituents of the tumor microenvironment. Several studies have delineated CAF heterogeneity in different types of tumors, however, it is still unknown how the distinct CAF transcriptional profiles are established during tumor progression. Methods: We reanalyzed a previously published single-cell RNA-sequencing dataset of MMTV-PyMT tumors at higher resolution using Seurat, and CytoTRACE to characterize CAF subtypes and their differentiation states. Wilcoxon rank sum test was applied for differential gene expression. Multiplex immunostaining (Akoya PhenoImager HT) was performed on 38 murine mammary tumors from MMTV-PyMT mice to identify the distinct CAF subtypes. Whole-slide... (More)
Background: Cancer-associated fibroblasts (CAFs) are the main constituents of the tumor microenvironment. Several studies have delineated CAF heterogeneity in different types of tumors, however, it is still unknown how the distinct CAF transcriptional profiles are established during tumor progression. Methods: We reanalyzed a previously published single-cell RNA-sequencing dataset of MMTV-PyMT tumors at higher resolution using Seurat, and CytoTRACE to characterize CAF subtypes and their differentiation states. Wilcoxon rank sum test was applied for differential gene expression. Multiplex immunostaining (Akoya PhenoImager HT) was performed on 38 murine mammary tumors from MMTV-PyMT mice to identify the distinct CAF subtypes. Whole-slide imaging and spatial analysis were conducted using QuPath and Cellpose, followed by neighborhood clustering and interaction mapping with CytoMAP. Cellular distances from CAFs to immune, tumor, and endothelial cells were quantified using SPIAT and Wilcoxon tests for comparisons. In parallel, human spatial transcriptomics data from the 10X Genomics Xenium platform were integrated for cross-species validation. Results: Here, by single cell RNA-sequencing and multiplex immunostaining, we identify six CAF substates. Spatial analysis on immunostained murine mammary tumors and human spatial transcriptomics data outlined temporal changes in stromal composition and the existence of distinct functional niches enriched with different CAF substates. Immunomodulatory CAFs co-localized with immune cells while myofibroblastic CAFs formed a shield around the tumor core, thus preventing immune infiltration. Conclusions: Our work supports the idea that distinct spatial locations dictate different CAF transcriptional programs. Targeting specific functional niches will ultimately hinder tumor progression by inhibiting signaling between distinct CAF substates and the surrounding tumor microenvironment. (Less)
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author
; ; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Breast cancer research : BCR
volume
28
article number
21
publisher
BioMed Central (BMC)
external identifiers
  • pmid:41521297
  • scopus:105028589367
ISSN
1465-5411
DOI
10.1186/s13058-025-02183-7
language
English
LU publication?
yes
id
d6d58562-82f7-4283-8fb1-02f742289141
date added to LUP
2026-01-19 08:14:59
date last changed
2026-04-21 03:00:09
@article{d6d58562-82f7-4283-8fb1-02f742289141,
  abstract     = {{Background: Cancer-associated fibroblasts (CAFs) are the main constituents of the tumor microenvironment. Several studies have delineated CAF heterogeneity in different types of tumors, however, it is still unknown how the distinct CAF transcriptional profiles are established during tumor progression. Methods: We reanalyzed a previously published single-cell RNA-sequencing dataset of MMTV-PyMT tumors at higher resolution using Seurat, and CytoTRACE to characterize CAF subtypes and their differentiation states. Wilcoxon rank sum test was applied for differential gene expression. Multiplex immunostaining (Akoya PhenoImager HT) was performed on 38 murine mammary tumors from MMTV-PyMT mice to identify the distinct CAF subtypes. Whole-slide imaging and spatial analysis were conducted using QuPath and Cellpose, followed by neighborhood clustering and interaction mapping with CytoMAP. Cellular distances from CAFs to immune, tumor, and endothelial cells were quantified using SPIAT and Wilcoxon tests for comparisons. In parallel, human spatial transcriptomics data from the 10X Genomics Xenium platform were integrated for cross-species validation. Results: Here, by single cell RNA-sequencing and multiplex immunostaining, we identify six CAF substates. Spatial analysis on immunostained murine mammary tumors and human spatial transcriptomics data outlined temporal changes in stromal composition and the existence of distinct functional niches enriched with different CAF substates. Immunomodulatory CAFs co-localized with immune cells while myofibroblastic CAFs formed a shield around the tumor core, thus preventing immune infiltration. Conclusions: Our work supports the idea that distinct spatial locations dictate different CAF transcriptional programs. Targeting specific functional niches will ultimately hinder tumor progression by inhibiting signaling between distinct CAF substates and the surrounding tumor microenvironment.}},
  author       = {{Pantaleo, Jessica and Sjölund, Jonas and Bolivar, Paulina and Bocci, Matteo and Phung, Bengt and Malmberg, Maria and Jönsson, Göran B and Pietras, Kristian}},
  issn         = {{1465-5411}},
  language     = {{eng}},
  publisher    = {{BioMed Central (BMC)}},
  series       = {{Breast cancer research : BCR}},
  title        = {{Spatial and temporal dynamics of cancer-associated fibroblast niches in breast cancer}},
  url          = {{http://dx.doi.org/10.1186/s13058-025-02183-7}},
  doi          = {{10.1186/s13058-025-02183-7}},
  volume       = {{28}},
  year         = {{2026}},
}