Gruosso, T. et al. Spatially distinct tumor immune microenvironments stratify triple-negative breast cancers. J. Clin. Invest. 129, 1785–1800 (2019).
Cox, T. R. The matrix in cancer. Nat. Rev. Cancer 21, 217–238 (2021).
Bejarano, L., Jordao, M. J. C. & Joyce, J. A. Therapeutic targeting of the tumor microenvironment. Cancer Discov. 11, 933–959 (2021).
Chen, Y. et al. Type I collagen deletion in αSMA+ myofibroblasts augments immune suppression and accelerates progression of pancreatic cancer. Cancer Cell 39, 548–565 (2021).
Leitinger, B. Discoidin domain receptor functions in physiological and pathological conditions. Int. Rev. Cell Mol. Biol. 310, 39–87 (2014).
Valiathan, R. R., Marco, M., Leitinger, B., Kleer, C. G. & Fridman, R. Discoidin domain receptor tyrosine kinases: new players in cancer progression. Cancer Metastasis Rev. 31, 295–321 (2012).
Hidalgo-Carcedo, C. et al. Collective cell migration requires suppression of actomyosin at cell-cell contacts mediated by DDR1 and the cell polarity regulators Par3 and Par6. Nat. Cell Biol. 13, 49–58 (2011).
Gao, H. et al. Multi-organ site metastatic reactivation mediated by non-canonical discoidin domain receptor 1 signaling. Cell 166, 47–62 (2016).
Edwards, D. N. et al. Selective glutamine metabolism inhibition in tumor cells improves anti-tumor T lymphocyte activity in triple-negative breast cancer. J Clin. Invest. 131, e140100 (2021).
Jiang, P. et al. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat. Med. 24, 1550–1558 (2018).
Jimenez-Sanchez, A., Cast, O. & Miller, M. L. Comprehensive benchmarking and integration of tumor microenvironment cell estimation methods. Cancer Res. 79, 6238–6246 (2019).
Vogel, W. F., Aszodi, A., Alves, F. & Pawson, T. Discoidin domain receptor 1 tyrosine kinase has an essential role in mammary gland development. Mol. Cell. Biol. 21, 2906–2917 (2001).
Takai, K. et al. Discoidin domain receptor 1 (DDR1) ablation promotes tissue fibrosis and hypoxia to induce aggressive basal-like breast cancers. Genes Dev. 32, 244–257 (2018).
Carafoli, F. et al. Structure of the discoidin domain receptor 1 extracellular region bound to an inhibitory Fab fragment reveals features important for signaling. Structure 20, 688–697 (2012).
Vogel, W. F. Ligand-induced shedding of discoidin domain receptor 1. FEBS Lett. 514, 175–180 (2002).
Agarwal, G., Mihai, C. & Iscru, D. F. Interaction of discoidin domain receptor 1 with collagen type 1. J. Mol. Biol. 367, 443–455 (2007).
Ruggeri, J. M. et al. Discoidin domain receptor 1 (DDR1) is necessary for tissue homeostasis in pancreatic injury and pathogenesis of pancreatic ductal adenocarcinoma. Am. J. Pathol. 190, 1735–1751 (2020).
Ambrogio, C. et al. Combined inhibition of DDR1 and Notch signaling is a therapeutic strategy for KRAS-driven lung adenocarcinoma. Nat. Med. 22, 270–277 (2016).
Salmon, H. et al. Matrix architecture defines the preferential localization and migration of T cells into the stroma of human lung tumors. J. Cell. Invest. 122, 899–910 (2021).
Kaur, A. et al. Remodeling of the collagen matrix in aging skin promotes melanoma metastasis and affects immune cell motility. Cancer Discov. 9, 64–81 (2019).
Ray, A. & Provenzano, P. P. Aligned forces: Origins and mechanisms of cancer dissemination guided by extracellular matrix architecture. Curr. Opin. Cell Biol. 72, 63–71 (2021).
Tomko, L. A. et al. Targeted matrisome analysis identifies thrombospondin-2 and tenascin-C in aligned collagen stroma from invasive breast carcinoma. Sci. Rep. 8, 12941 (2018).
Dunlap, S. M. et al. Dietary energy balance modulates epithelial-to-mesenchymal transition and tumor progression in murine claudin-low and basal-like mammary tumor models. Cancer Prev. Res. 5, 930–942 (2012).
Mertins, P. et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature 534, 55–62 (2016).
Hanzelmann, S., Castelo, R. & Guinney, J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 14, 7 (2013).
Fougner, C., Bergholtz, H., Norum, J. H. & Sorlie, T. Re-definition of claudin-low as a breast cancer phenotype. Nat. Commun. 11, 1787 (2020).
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2000).
Suzuki, R. & Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540–1542 (2006).
Raudvere, U. et al. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists. Nucleic Acids Res. 47, W191–W198 (2019).
Li, T. et al. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res. 48, W509–W514 (2020).
Newman, A. M. et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat. Biotechnol. 37, 773–782 (2019).
Erikson, A., Ortegren, J., Hompland, T., de Lange Davies, C. & Lindgren, M. Quantification of the second-order nonlinear susceptibility of collagen I using a laser scanning microscope. J. Biomed. Opt. 12, 044002 (2007).
Wu, B. et al. PPARγ inhibition boosts efficacy of immune checkpoint immunotherapy against murine melanoma in a sexually dimorphic manner. Int. J. Biol. Sci. 16, 1526–1535 (2020).
Meng, W. et al. Efficient generation of monoclonal antibodies from single rhesus macaque antibody secreting cells. MAbs 7, 707–718 (2015).
Gui, X. et al. Disrupting LILRB4/APOE interaction by an efficacious humanized antibody reverses T-cell suppression and blocks AML development. Cancer Immunol. Res. 7, 1244–1257 (2019).
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