Spatially and Functionally Distinct Subclasses of Breast Cancer-associated Fibroblasts Revealed by Single Cell RNA Sequencing

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Dec 6

PMID 30514914

Citations 408

Authors

Michael Bartoschek

Nikolay Oskolkov

Matteo Bocci

John Lovrot

Christer Larsson

Mikael Sommarin

Chris D Madsen

David Lindgren

Gyula Pekar

Goran Karlsson

Markus Ringner

Jonas Bergh

Asa Bjorklund

Kristian Pietras

Affiliations

Soon will be listed here.

Abstract

Cancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment, although their origin and roles in shaping disease initiation, progression and treatment response remain unclear due to significant heterogeneity. Here, following a negative selection strategy combined with single-cell RNA sequencing of 768 transcriptomes of mesenchymal cells from a genetically engineered mouse model of breast cancer, we define three distinct subpopulations of CAFs. Validation at the transcriptional and protein level in several experimental models of cancer and human tumors reveal spatial separation of the CAF subclasses attributable to different origins, including the peri-vascular niche, the mammary fat pad and the transformed epithelium. Gene profiles for each CAF subtype correlate to distinctive functional programs and hold independent prognostic capability in clinical cohorts by association to metastatic disease. In conclusion, the improved resolution of the widely defined CAF population opens the possibility for biomarker-driven development of drugs for precision targeting of CAFs.

Citing Articles

The multi-faceted immune modulatory role of S100A4 in cancer and chronic inflammatory disease.

Wong T, Kang R, Yun K Front Immunol. 2025; 16:1525567.

PMID: 40078995 PMC: 11897520. DOI: 10.3389/fimmu.2025.1525567.

Quantifying and interpreting biologically meaningful spatial signatures within tumor microenvironments.

Jing S, Wang H, Lin P, Yuan J, Tang Z, Li H NPJ Precis Oncol. 2025; 9(1):68.

PMID: 40069556 PMC: 11897387. DOI: 10.1038/s41698-025-00857-1.

Analyze the Diversity and Function of Immune Cells in the Tumor Microenvironment From the Perspective of Single-Cell RNA Sequencing.

Ma L, Luan Y, Lu L Cancer Med. 2025; 14(5):e70622.

PMID: 40062730 PMC: 11891933. DOI: 10.1002/cam4.70622.

Hidradenitis Suppurativa Tunnels: Unveiling a Unique Disease Entity.

Vecin N, Balukoff N, Yaghi M, Gonzalez T, Sawaya A, Strbo N JID Innov. 2025; 5(3):100350.

PMID: 40034103 PMC: 11872476. DOI: 10.1016/j.xjidi.2025.100350.

Development of a phenotypic screening assay to measure activation of cancer-associated fibroblasts.

Ilg M, Lapthorn A, Harding S, Minhas T, Koduri G, Bustin S Front Pharmacol. 2025; 16:1526495.

PMID: 40017592 PMC: 11865240. DOI: 10.3389/fphar.2025.1526495.

References

Costa A, Kieffer Y, Scholer-Dahirel A, Pelon F, Bourachot B, Cardon M . Fibroblast Heterogeneity and Immunosuppressive Environment in Human Breast Cancer. Cancer Cell. 2018; 33(3):463-479.e10. DOI: 10.1016/j.ccell.2018.01.011. View

Winslow S, Lindquist K, Edsjo A, Larsson C . The expression pattern of matrix-producing tumor stroma is of prognostic importance in breast cancer. BMC Cancer. 2016; 16(1):841. PMC: 5095990. DOI: 10.1186/s12885-016-2864-2. View

Cunha S, Bocci M, Lovrot J, Eleftheriou N, Roswall P, Cordero E . Endothelial ALK1 Is a Therapeutic Target to Block Metastatic Dissemination of Breast Cancer. Cancer Res. 2015; 75(12):2445-56. DOI: 10.1158/0008-5472.CAN-14-3706. View

Pietras K, Ostman A . Hallmarks of cancer: interactions with the tumor stroma. Exp Cell Res. 2010; 316(8):1324-31. DOI: 10.1016/j.yexcr.2010.02.045. View

Farmer P, Bonnefoi H, Anderle P, Cameron D, Wirapati P, Wirapati P . A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer. Nat Med. 2009; 15(1):68-74. DOI: 10.1038/nm.1908. View

Lun A, McCarthy D, Marioni J . A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res. 2016; 5:2122. PMC: 5112579. DOI: 10.12688/f1000research.9501.2. View

Ramskold D, Wang E, Burge C, Sandberg R . An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol. 2009; 5(12):e1000598. PMC: 2781110. DOI: 10.1371/journal.pcbi.1000598. View

Tirosh I, Izar B, Prakadan S, Wadsworth 2nd M, Treacy D, Trombetta J . Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016; 352(6282):189-96. PMC: 4944528. DOI: 10.1126/science.aad0501. View

Cortez E, Roswall P, Pietras K . Functional subsets of mesenchymal cell types in the tumor microenvironment. Semin Cancer Biol. 2014; 25:3-9. DOI: 10.1016/j.semcancer.2013.12.010. View

10.

LeBleu V, Taduri G, OConnell J, Teng Y, Cooke V, Woda C . Origin and function of myofibroblasts in kidney fibrosis. Nat Med. 2013; 19(8):1047-53. PMC: 4067127. DOI: 10.1038/nm.3218. View

11.

Zeisberg E, Potenta S, Xie L, Zeisberg M, Kalluri R . Discovery of endothelial to mesenchymal transition as a source for carcinoma-associated fibroblasts. Cancer Res. 2007; 67(21):10123-8. DOI: 10.1158/0008-5472.CAN-07-3127. View

12.

Uhlen M, Fagerberg L, Hallstrom B, Lindskog C, Oksvold P, Mardinoglu A . Proteomics. Tissue-based map of the human proteome. Science. 2015; 347(6220):1260419. DOI: 10.1126/science.1260419. View

13.

Naba A, Clauser K, Hoersch S, Liu H, Carr S, Hynes R . The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Mol Cell Proteomics. 2011; 11(4):M111.014647. PMC: 3322572. DOI: 10.1074/mcp.M111.014647. View

14.

Ozdemir B, Pentcheva-Hoang T, Carstens J, Zheng X, Wu C, Simpson T . Depletion of carcinoma-associated fibroblasts and fibrosis induces immunosuppression and accelerates pancreas cancer with reduced survival. Cancer Cell. 2014; 25(6):719-34. PMC: 4180632. DOI: 10.1016/j.ccr.2014.04.005. View

15.

Hamilton T, Klinghoffer R, Corrin P, Soriano P . Evolutionary divergence of platelet-derived growth factor alpha receptor signaling mechanisms. Mol Cell Biol. 2003; 23(11):4013-25. PMC: 155222. DOI: 10.1128/MCB.23.11.4013-4025.2003. View

16.

Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G . Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res. 2008; 14(16):5158-65. DOI: 10.1158/1078-0432.CCR-07-4756. View

17.

Rhim A, Oberstein P, Thomas D, Mirek E, Palermo C, Sastra S . Stromal elements act to restrain, rather than support, pancreatic ductal adenocarcinoma. Cancer Cell. 2014; 25(6):735-47. PMC: 4096698. DOI: 10.1016/j.ccr.2014.04.021. View

18.

Guy C, Webster M, Schaller M, Parsons T, Cardiff R, Muller W . Expression of the neu protooncogene in the mammary epithelium of transgenic mice induces metastatic disease. Proc Natl Acad Sci U S A. 1992; 89(22):10578-82. PMC: 50384. DOI: 10.1073/pnas.89.22.10578. View

19.

Roswall P, Bocci M, Bartoschek M, Li H, Kristiansen G, Jansson S . Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling. Nat Med. 2018; 24(4):463-473. PMC: 5896729. DOI: 10.1038/nm.4494. View

20.

Pereira B, Chin S, Rueda O, Vollan H, Provenzano E, Bardwell H . The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nat Commun. 2016; 7:11479. PMC: 4866047. DOI: 10.1038/ncomms11479. View