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ORIGINAL RESEARCH
Transcriptomic features of FAP+ cells across molecular subtypes of breast cancer
Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
Correspondence should be addressed: Evgeniya S. Grigoryeva
Koperativny Lane, str. 7, Tomsk, 634009, Russia; moc.liamg@se.aveyrogirg
Funding: this work was supported by the Russian Science Foundation (grant No. 25-65-00021).
Author contribution: Kalinchuk AYu — writing and formatting; Patskan IA — bioinformatic analysis; Shtadelman MM — data collection and analysis; Grigoryeva ES — interpretation of results; Tashireva LA — interpretation of results, concept development. All authors participated in the final editing of the article.
Compliance with ethical standards: The study was approved by the Ethics Committee of the Tomsk National Research Medical Center of Oncology (Protocol No. 3 dated August 25, 2020). The work was conducted in accordance with the principles of the Helsinki Declaration (1964) and its amendments (1975 and 1983). All patients provided written informed consent to participate in the study.
Understanding subtype-specific variability of functional programs in FAP+ tumor-associated fibroblasts (TAFs) is fundamental for developing effective therapeutic strategies targeting stromal components. The aim of this study was to identify subtype-specific signaling pathways, markers, and molecular features of FAP+ TAFs. Using spatial transcriptomic analysis, we demonstrated that FAP+ TAFs in luminal breast cancer exhibit a phenotype characterized by extracellular matrix organization (GO:0030198, FDR q-value = 0.0307) and expression of genes associated with metastasis (COL10A1, MMP13, CXCL14, TSPAN8). In contrast, FAP+ TAFs in triple-negative breast cancer display a pronounced immunomodulatory phenotype with overexpression of immunosuppressive genes (CD36, PLA2G2A, CHI3L1) and enrichment of immune response-related pathways (immune response (GO:0006955, FDR q-value = 7.85e-17), inflammatory response (GO:0006954, FDR q-value = 2.79e-11), regulation of cytokine production (GO:0001817, FDR q-value = 3.39e-10)). We also identified subtype-specific gene signatures related to radioresistance: luminal A and B subtypes showed activation of DNA repair pathways (IGF1R, ERBB3, CRIP1), while triple-negative tumors demonstrated enrichment of epithelial-mesenchymal transition and stemness markers (ZEB2, NOTCH4, FOXM1). These findings emphasize that FAP+ fibroblasts are not a homogeneous population but functionally specialize depending on tumor subtype — acting as stromal architects in luminal breast cancer and as regulators of immune response in triple-negative breast cancer.
Keywords: breast cancer, fibroblasts, tumor microenvironment, spatial transcriptomics